WO2006079176A1 - Molecules et leurs molecules chimeriques - Google Patents

Molecules et leurs molecules chimeriques Download PDF

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WO2006079176A1
WO2006079176A1 PCT/AU2006/000102 AU2006000102W WO2006079176A1 WO 2006079176 A1 WO2006079176 A1 WO 2006079176A1 AU 2006000102 W AU2006000102 W AU 2006000102W WO 2006079176 A1 WO2006079176 A1 WO 2006079176A1
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protein
chimeric molecule
cells
molecule
cell
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PCT/AU2006/000102
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John D. Priest
Alan D. Watts
Jason S. Whittaker
Teresa A. Domagala
Glenn R. Pilkington
Ingrid Boehm
Carol M. Y. Lee
Mei Ann Lim
Nikolien S. Thomas
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Apollo Life Sciences Limited
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Priority claimed from AU2005906366A external-priority patent/AU2005906366A0/en
Application filed by Apollo Life Sciences Limited filed Critical Apollo Life Sciences Limited
Priority to US11/814,566 priority Critical patent/US20090232808A1/en
Priority to JP2007552463A priority patent/JP2008528006A/ja
Priority to AU2006208439A priority patent/AU2006208439A1/en
Priority to EP06704788A priority patent/EP1844069A4/fr
Priority to CA002596537A priority patent/CA2596537A1/fr
Publication of WO2006079176A1 publication Critical patent/WO2006079176A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70575—NGF/TNF-superfamily, e.g. CD70, CD95L, CD153, CD154
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K38/00—Medicinal preparations containing peptides
    • A61K38/16—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • A61K38/17—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • A61K38/19—Cytokines; Lymphokines; Interferons
    • A61K38/191—Tumor necrosis factors [TNF], e.g. lymphotoxin [LT], i.e. TNF-beta
    • A—HUMAN NECESSITIES
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61P17/00—Drugs for dermatological disorders
    • A61P17/04—Antipruritics
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A61P17/06—Antipsoriatics
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P17/00—Drugs for dermatological disorders
    • A61P17/16—Emollients or protectives, e.g. against radiation
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P19/00—Drugs for skeletal disorders
    • A61P19/02—Drugs for skeletal disorders for joint disorders, e.g. arthritis, arthrosis
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61P25/00—Drugs for disorders of the nervous system
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    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/02—Drugs for disorders of the nervous system for peripheral neuropathies
    • A—HUMAN NECESSITIES
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    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/14—Drugs for disorders of the nervous system for treating abnormal movements, e.g. chorea, dyskinesia
    • A61P25/16—Anti-Parkinson drugs
    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P25/00—Drugs for disorders of the nervous system
    • A61P25/28—Drugs for disorders of the nervous system for treating neurodegenerative disorders of the central nervous system, e.g. nootropic agents, cognition enhancers, drugs for treating Alzheimer's disease or other forms of dementia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P29/00—Non-central analgesic, antipyretic or antiinflammatory agents, e.g. antirheumatic agents; Non-steroidal antiinflammatory drugs [NSAID]
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    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/04—Antibacterial agents
    • A61P31/08—Antibacterial agents for leprosy
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P31/00—Antiinfectives, i.e. antibiotics, antiseptics, chemotherapeutics
    • A61P31/10—Antimycotics
    • A—HUMAN NECESSITIES
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    • A61P35/00—Antineoplastic agents
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    • A61P37/02—Immunomodulators
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    • A61P37/02—Immunomodulators
    • A61P37/06—Immunosuppressants, e.g. drugs for graft rejection
    • A—HUMAN NECESSITIES
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    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61P9/00—Drugs for disorders of the cardiovascular system
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/525—Tumour necrosis factor [TNF]
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/52—Cytokines; Lymphokines; Interferons
    • C07K14/525—Tumour necrosis factor [TNF]
    • C07K14/5255—Lymphotoxin [LT]
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
    • G01N33/6863—Cytokines, i.e. immune system proteins modifying a biological response such as cell growth proliferation or differentiation, e.g. TNF, CNF, GM-CSF, lymphotoxin, MIF or their receptors

Definitions

  • the present invention relates generally to the fields of proteins, diagnostics, therapeutics and nutrition. More particularly, the present invention provides an isolated protein molecule in or related to the tumour necrosis factor (TNF) superfamily such as TNF-a, Lymphotoxin-a (LT-a), TNFRI, TNFRII, OX40, BAFF, NGFR, Fas Ligand or chimeric molecules thereof comprising at least a portion of the protein molecule, such as TNF-a-Fc, LT-a-Fc, TNFRI-Fc, TNFRII-Fc, OX40-Fc, BAFF-Fc, NGFR-Fc, Fas Ligand-Fc; wherein the protein or chimeric molecule thereof has a profile of measurable physiochemical parameters, wherein the profile is indicative of, associated with or forms the basis of one or more pharmacological traits.
  • TNF tumour necrosis factor
  • LT-a Lymphotoxin-a
  • Fas Ligand Fas Ligand or chimeric
  • TNF superfamily is associated with the regulation of cell growth, survival, apoptosis and necrosis, as well as inflammatory responses. Significantly, TNF molecules have a selective cytotoxic effect on tumour cells as well as inducing apoptosis in non-cancerous cells. Receptors in the TNF superfamily contain cysteine-rich repeats in the extra-cellular domain. Members of the TNF superfamily include TNF-a, LT-a, TNFRI, TNFRII, OX40, BAFF, NGFR and Fas Ligand. TNF-a (TNF-alpha, tumour necrosis factor ligand superfamily member 2, TNFSF2) is a 233 amino acid membrane-bound protein that forms a biologically active homotrimer.
  • lymphotoxin alpha (LT-a, TNF beta, TNFSF2) is synthesised as a 205 amino acid peptide including a 34 amino acid signal sequence that, unlike the other TNF superfamily ligands, directs the secretion of its mature peptide.
  • TNF-a and LT-a mediate necrosis or apoptosis particularly in transformed cells, as well as the induction of inflammatory processes, cell proliferation, cytokine release and activation of T and B lymphocytes. Additionally, localized, low-level expression of TNF-a and LT-a participates in tissue re-modelling and host defence responses, including the destruction virus infected cells and enhancement of antibacterial activities of granulocytes. Additionally, during embryonic development TNF-a and LT-a have been identified as a key component in the organogenesis of the peripheral lymphatic organ system, such as lymph nodes, spleen and Peyer's patches. Uncontrolled regulation of TNF-a or LT-a expression plays a major role in the development of autoimmune diseases such as rheumatoid arthritis, and inflammatory bowel diseases, such as Crohn's disease and multiple sclerosis (MS).
  • autoimmune diseases such as rheumatoid arthritis
  • MS multiple sclerosis
  • TNF-a and LT-a are mediated through the TNF receptors, tumor necrosis factor receptor I (TNFRI) and tumor necrosis factor receptor II (TNFRII). Both TNF receptors bind TNF-a and LT-a with high affinity and are present on virtually all cell types except for red blood cells. Deletion analysis in the C terminal intracellular region of TNFRI has revealed the existence of a death domain, which is involved in signalling processes leading to programmed cell death. The death domain of TNFRI interacts with a variety of other signalling adaptor molecules, including TRADD and RIP. TNFRII is more abundant on endothelial cells and cells of hematopoietic lineage.
  • TNFRII Soluble forms of TNFRII have been characterized in human urine as 3OkDa and 45kDa proteins. These soluble TNF receptor proteins exhibit TNF inhibitory qualities and result from the proteolytic cleavage of the membrane bound receptor. Notably, many of the stimuli that induce expression of TNF-a also induced expression of soluble TNF receptors suggesting the soluble receptors may play a role in regulating TNF activity.
  • TNFRI and TNFRII may be useful for treating a disease state in a subject which is characterized by an excess of TNF- a, for example, psoriasis. Psoriasis is currently affecting approximately 2-3% of the population worldwide (Nickoloff et al. J Clin Invest.
  • psoriasis is much more than a dermatological nuisance, as it interferes with many normal daily activities, such as the use of hands, walking, sleeping, and sexual activity. It is reported that at least 30% of psoriasis patients actually contemplate suicide (Nickoloff et al, supra, 2004).
  • TNF-a inflammatory skin conditions characterized by an excess level of TNF-a
  • Behcet's disease bullous dermatitis, eczema, fungal infection, leprosy, neutrophilic dermatitis, pityriasis maculara (or pityriasis rosea), pityriasis nigra (or tinea nigra), pityriasis rubra pilaris, systemic lupus erythematosus, systemic vascularitis and toxic epidermal necrolysis (Evereklioglu Expert Opin Pharmacother 5(2) :317-28, 2004; Lipoquelc et al.
  • Human OX40 (tumor necrosis factor receptor superfamily member 4, TNFSF4) is a 50 kDa transmembrane protein expressed primarily on the surface of activated CD4+ T cells.
  • OX40 is a co-stimulatory molecule involved in the T cell dependent immune response, namely, T cell activation and proliferation, the induction of cytokine production by effector T cells, generation of memory T cells, and arresting peripheral T cell tolerance in vivo. Expression of OX40 is induced hours or days following the initiation of a CD28 signal. It has been reported that the interaction of OX40 with its ligand plays a role in the expansion of T cell numbers at the height of the immune response as well as the generation of memory T cells.
  • OX40-OX40L interactions also mediate T-cell proliferation and IL-2 production in the absence of CD28.
  • activated OX40 deficient T cells are highly susceptible to apoptosis despite having relatively normal IL-2 production, cell division and expansion. It has been proposed that manipulating the levels of OX40 or OX40-OX40L interaction during inflammatory responses may be therapeutically beneficial in T-cell mediated diseases especially allergic, inflammatory and autoimmune diseases.
  • BAFF tumor necrosis factor ligand superfamily member 13B, TNFSF 13B
  • TNFSF 13B tumor necrosis factor ligand superfamily member 13B
  • BAFF is a 285 amino acid type II membrane glycoprotein. BAFF is expressed by B cells, T cells, dendritic cells, macrophages and neutrophils. BAFF is a B cell survival factor and specifically promotes the proliferation of activated B cells, Immunoglobulin switching to IgD + B cells, the survival of immunoglobulin secreting cells and is involved in B cell maturation. This suggests BAFF is an important mediator of the humoral immune response. Studies indicate that treatment of B cells with BAFF results in the expression of pro-survival oncogenes including Bcl-xL, Bcl-2 and McI-I.
  • BAFF is a B cell survival factor, its de-regulation can promote the survival of auto-reactive B cells and the pathogenesis of autoimmune disease. Additionally, elevated levels of BAFF have also been detected in patients with autoimmune disease, including in the joints of patients with rheumatoid arthritis (RA) and inflammatory arthritis where the synovial levels of BAFF are higher than serum levels.
  • BAFF is useful for regulating biological processes mediated by B cells, T cells, dendritic cells, macrophages and neutrophils, in particular for activating the BAFFR e.g. to increase B-lymphocyte proliferation, activation and survival.
  • BAFF can be used as a treatment for immune deficiency, e.g.
  • BAFF can also be used to enhance antibody production in vaccination procedures. Additionally, BAFF linked to radionuclides can be as therapy for targetting and killing B-cell malignancies.
  • Nerve growth factor receptor also is tumour necrosis factor receptor superfamily member 16 TNFRSF 16.
  • NGFR is a type I membrane protein that is synthesised as a 427 amino acid glycoprotein consisting of a 28 amino acid signal peptide.
  • NGFR binds with equal affinity all neurotrophins, but higher affinity binding is achieved by association of NGFR with TrkA, B and C.
  • Ligand binding to the NGFR can promote either survival or apoptosis of neurons.
  • the effects neurotrophins on cells involves a complex interplay between the NGFR receptor and the Trk A, B and C receptors that is not completely understood.
  • NGF treatment of neurons induces apoptosis, which is not seen in neurons deficient in NGFR, while Trk A predominantly inhibits NGFR apoptotic activity.
  • Trk A predominantly inhibits NGFR apoptotic activity.
  • a further complexity is that both the pro-apoptotic and anti-apoptotic pathways induced by NGFR signalling are dependent upon the type and functional state of the cell.
  • Fas Ligand (FasL or TNF ligand superfamily member 6, TNFSF6) is a 281 amino acid type II membrane protein. FasL also exist as a soluble protein resulting from proteolytic cleavage of the ECD or by alternative splicing. The active form of FasL is homotrimeric. FasL is involved in the regulation of programmed cell death (apoptosis), immune homeostasis and immune privilege and tumor cell survival. Initial experiments showed that activated CD4+ T cells induced cytolytic activity in cells expressing Fas. FasL was subsequently cloned and was demonstrated to induce apoptosis via interaction with Fas.
  • FasL plays an important role in normal immune homeostasis as FasL deficient animal models develop systemic autoimmune disease.
  • FasL has been identified as being involved in three types of apoptosis: the removal of activated T cells at the end of an immune response; the killing of virally infected or cancerous cells by cytolytic T cells or natural killer cells; and the killing of inflammatory cells by non-lymphoid cells in the eye and testis. Additionally, FasL expression can also promote neutrophil-mediated inflammatory responses via a neutrophilic chemotactic activity. Additionally, FasL is involved in erythroid differentiation, angiogenesis e.g. in the eye and skin homeostasis and the response to cellular stress.
  • the biological effector functions exerted by proteins via interaction with their respective binding proteins means that the TNF superfamily and its related proteins and their respective ligands or receptors may have significant potential as therapeutic agents to modulate physiological processes.
  • minor changes to the molecule such as primary, secondary, tertiary or quaternary structure and co- or post-translational modification patterns can have a significant impact on the activity, secretion, antigenicty and clearance of the protein.
  • the proteins can be generated with specific primary, secondary, tertiary or quaternary structure, or co- or post- translational structure or make-up that confer unique or particularly useful properties.
  • proteins produced from these non-human expression systems will exhibit physiochemical and pharmacological characteristics such as half-life, antigenicity,stability and functional potency that are distinct from human cell-derived proteins.
  • stem cell technology has substantially increased the potential for utilizing stem cells in applications such as transplantation therapy, drug screening, toxicology studies and functional genomics.
  • stem cells are routinely maintained in culture medium that contains non-human proteins and are therefore not suitable for clinical applications due to the possibility of contamination with non-human infectious material.
  • culturing of stem cells in non-human derived media may result in the incorporation of non-human carbohydrate moieties thus compromising transplant application. (Martin et al. Nature Medicine 11 (2) /228-232, 2005).
  • the use of specific human-derived proteins in the maintenance and/or differenttiation of stem cells will ameliorate the incorporation of xenogeneic proteins and enhance stem cell clinical utility.
  • SEQ ID NO: Nucleotide and amino acid sequences are referred to by a sequence identifier number (SEQ ID NO:).
  • the SEQ ID NOs: correspond numerically to the sequence identifiers ⁇ 400>l (SEQ ID NO:1), ⁇ 400>2 (SEQ ID NO:2), etc.
  • SEQ ID NO:1 sequence identifiers ⁇ 400>l
  • SEQ ID NO:2 sequence identifiers
  • the present invention relates generally to an isolated protein or chimeric molecule thereof in or related to the TNF superfamily comprising a profile of physiochemical parameters, wherein the profile is indicative of, associated with, or forms the basis of one or more distinctive pharmacological traits. More particularly, the present invention provides an isolated protein or chimeric molecule thereof selected from the list of TNF-a, TNF-a-Fc, LT-a, LT-a-Fc, TNFRI, TNFRI-Fc, TNFRII, TNFRII-Fc, OX40, OX40-Fc, BAFF, BAFF- Fc, NGFR, NGFR-Fc, Fas Ligand, Fas Ligand-Fc comprising a physiochemical profile comprising a number of measurable physiochemical parameters, ⁇ [P x ]i, [P x ]2,- --[P x ]n, ⁇ , wherein P x represents a measurable physiochemical parameter and "n" is an integer >1, wherein each
  • the term "distinctive" with regard to a pharmacological trait of a protein or chimeric molecule thereof of the present invention refers to one or more pharmacological traits of a protein or chimeric molecule thereof which are distinctive for the particular physiochemical profile.
  • one or more of the pharmacological traits of an isolated protein or chimeric molecule thereof is different from, or distinctive relative to a form of the same protein or chimeric molecule thereof produced in a prokaryotic or lower eukaryotic cell or even a higher eukaryotic cell of a non-human species.
  • the pharmacological traits of a subject isolated protein or chimeric molecule thereof contribute to a desired functional outcome.
  • measurable physiochemical parameters refers to one or more measurable characteristics of the isolated protein or chimeric molecule thereof.
  • the measurable physiochemical parameters of a subject isolated protein or chimeric molecule thereof contribute to or are otherwise responsible for the derived pharmacological trait, Ty.
  • An isolated protein or chimeric molecule of the present invention comprises physiochemical parameters (P x ) which taken as a whole define protein molecule or chimeric molecule.
  • the physiochemical parameters may be selected from the group consisting of apparent molecular weight (P 1 ), isoelectric point (pi) (P 2 ), number of isoforms (P 3 ), relative intensities of the different number of isoforms (P 4 ), percentage by weight carbohydrate (P 5 ), observed molecular weight following N-linked oligosaccharide deglycosylation (P 6 ), observed molecular weight following N-linked and O-linked oligosaccharide deglycosylation (P 7 ), percentage acidic monosaccharide content (P 8 ), monosaccharide content (P 9 ), sialic acid content (P 1 O), sulfate and phosphate content (P 11 ), Ser/Thr : GaINAc ratio (P 12 ), neutral percentage of N-linked oligosaccharide content (
  • a TNF-a of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
  • P 1 apparent molecular weight of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
  • a LT-a of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: - an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
  • a TNFRI-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 5 to 120 kD such as 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
  • P 1 apparent molecular weight of about 5 to 120 kD such as 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57,
  • N-linked oligosaccharides P 14
  • P 14 an acidic percentage of N-linked oligosaccharides (P 14 ) of about 0 to 50% such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50%, and in one embodiment 0 to 20% , and a further embodiment, 3 to 6%; - a neutral percentage of O-linked oligosaccharides (P 15 ) of about 24 to 67% such as 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61%, and
  • a TNFRII-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 10 to 150, such as 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
  • 10-40 isoforms; a percentage by weight carbohydrate (P 5 ) of about 0 to 99%, such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98
  • an observed molecular weight of the molecule after the N-linked oligosaccharides are removed (P 6 ) of about 40 to 100 kDa and in one embodiment, 46 to 87 kDa; an observed molecular weight of the molecule after the N-linked and O-linked oligosaccharides are removed (P 7 ) of about 40 to 95 kDa and in one embodiment, 42 to 80 kDa; a percentage acidic monosaccharide content (P 8 ) of about 0 to 50%, such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, and in one embodiment, 1 to 10 %; monosaccharide (P 9 ) and sialic acid (P 10 ) contents of, when normalized to GaINA
  • O-linked oligosaccharides P 15
  • P 15 O-linked oligosaccharides
  • TNFRII-Fc one or more O-glycan structures as listed in Table 37(b) in the O-linked fraction (P 20 ); a biological activity that is distinct from that of a human TNFRII-Fc expressed in a non-human cell system, and in one embodiment, the ability of TNFRII-Fc of the present invention to neutralise TNF-a induced cytotoxicity (T 30 ) in L-929 cells is 8- 18 fold more potent than a human TNFRII-Fc expressed in E. coli cells.
  • an OX40-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (Ty) comprising: - an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9,
  • a BAFF of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94
  • a NGFR-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
  • a Fas Ligand of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
  • N-linked oligosaccharides P 6
  • P 21 N-linked oligosaccharides
  • the present invention contemplates an isolated form of protein or chimeric molecule thereof in or related to the TNF superfamily selected from the group comprising TNF-a, TNF-a-Fc, LT-a, LT-a-Fc, TNFRI, TNFRI-Fc, TNFRII, TNFRII-Fc, OX40, OX40-Fc, BAFF, BAFF-Fc, NGFR, NGFR-Fc, Fas Ligand, Fas Ligand-Fc.
  • An isolated protein or chimeric molecule of the present invention comprises distinctive pharmacological traits selected from the group comprising or consisting of therapeutic efficiency (T 1 ), effective therapeutic dose (TCID 50 ) (T 2 ), bioavailability (T 3 ), time between dosages to maintain therapeutic levels (T 4 ), rate of absorption (T 5 ), rate of excretion (T 6 ), specific activity (T 7 ), thermal stability (T 8 ), lyophilization stability (T 9 ), serum/plasma stability (T 10 ), serum half-life (T 11 ), solubility in blood stream (T 12 ), immunoreactivity profile (T 13 ), immunogenicity (T 14 ), inhibition by neutralizing antibodies (T 14 A), side effects (T 15 ), receptor/ligand binding affinity (T 16 ), receptor/ligand activation (T 17 ), tissue or cell type specificity (T 18 ), ability to cross biological membranes or barriers (i.e.
  • T 19 gut, lung, blood brain barriers, skin etc
  • T 19A angiogenic ability
  • T 20 tissue uptake
  • T 21 stability to degradation
  • T 22 stability to freeze-thaw
  • T 23 stability to proteases
  • T 24 ease of administration
  • T 25 ease of administration
  • T 26 compatibility with other pharmaceutical excipients or carriers
  • T 28 persistence in organism or environment
  • T 29 stability in storage
  • T 30 toxicity in an organism or environment and the like
  • the protein or chimeric molecule of the present invention may have altered biological effects on different cells types (T 31 ), including without being limited to human primary cells, such as lymphocytes, erythrocytes, retinal cells, hepatocytes, neurons, keratinocytes, endothelial cells, endodermal cells, ectodermal cells, mesodennal cells, epithelial cells, kidney cells, liver cells, bone cells, bone marrow cells, lymph node cells, dermal cells, fibroblasts, T-cells, B-cells, plasma cells, natural killer cells, macrophages, granulocytes, neutrophils, Langerhans cells, dendritic cells, eosinophils, basophils, mammary cells, lobule cells, prostate cells, lung cells, oesophageal cells, pancreatic cells, Beta cells (insulin secreting cells), hemangioblasts, muscle cells, oval cells (hepatocytes), mesenchymal cells, brain
  • the biological effects on the cells include effects on proliferation (T 32 ), differentiation (T 33 ), apoptosis (T 34 ), growth in cell size (T 35 ), cytokine adhesion (T 36 ), cell adhesion (T 37 ), cell spreading (T 38 ), cell motility (T 39 ), migration and invasion (T 40 ), chemotaxis (T 41 ), cell engulfment (T 42 ), signal transduction (T 43 ), recruitment of proteins to receptors/ligands (T 44 ), activation of the JAK/STAT pathway (T 45 ), activation of the Ras- erk pathway (T 46 ), activation of the AKT pathway (T 47 ), activation of the PKC pathway (T 48 ), activation of the PKA pathway (T 49 ), activation of src (T 50 ), activation of fas (T 51 ), activation of TNFR (T 52 ), activation of NFkB (T 53 ), activation of p38MAPK (T 54
  • the present invention further provides a chimeric molecule comprising an isolated protein or a fragment thereof, such as an extra-cellular domain of a membrane bound protein, linked to the constant (Fc) or framework region of a human immunoglobulin via one or more protein linker.
  • a chimeric molecule is also referred to herein as protein-Fc.
  • protein-Fc contemplated by the present invention include TNF-a-Fc, LT- a-Fc, TNFRI-Fc, TNFRII-Fc, OX40-Fc, BAFF-Fc, NGFR-Fc, Fas Ligand-Fc.
  • Such protein-Fc has a profile of measurable physiochemical parameters indicative of or associated with one or more distinctive pharmacological traits of the isolated protein-Fc.
  • Other chimeric molecules contemplated by the present invention include the protein or protein-Fc or a fragment thereof, linked to a lipid moiety such as a polyunsaturated fatty acid molecule. Such lipid moieties may be linked to an amino acid residue in the backbone of the molecule or to a side chain of such an amino acid residue.
  • the present invention further provides a chimeric molecule comprising an isolated protein or a fragment thereof, such as an extra-cellular domain of a membrane bound protein, linked to the constant (Fc) or framework region of a mammalian immunoglobulin via one or more protein linker.
  • the mammal Fc or framework region of the immunoglobulin is derived from a mammal selected from the group consisting of primates, including humans, marmosets, orangutans and gorillas, livestock animals (e.g. cows, sheep, pigs, horses, donkeys), laboratory test animals (e.g. mice, rats, guinea pigs, hamsters, rabbits, companion animals (e.g.
  • the Fc or framework region is a human immunoglobulin.
  • the mammal is a human.
  • Such a chimeric molecule is also referred to herein as protein-Fc.
  • Other chimeric molecules contemplated by the present invention include the protein or protein-Fc or a fragment thereof linked to a lipid moiety such as a polyunsaturated fatty acid molecule. Such lipid moieties may be linked to an amino acid residue in the background of the molecule or to a side chain of such an amino acid residue.
  • the chimeric molecules of the present invention including TNF-a-Fc, LT-a-Fc, TNFRI-Fc, TNFRII-Fc, OX40-Fc, BAFF-Fc, NGFR-Fc, Fas Ligand-Fc have a profile of measurable physiochemical parameters indicative of or associated with one or more distinctive pharmacological traits of the isolated protein-Fc.
  • TNFRI-Fc and “TNFRII-Fc” refer to the fusion of a fragment of the TNFR polypeptide (e.g. TNFRI or TNFRII) comprising one or more extracellular domains of TNFRI or TNFRII, linked directly or via one or more protein linkers known in the art to a constant (Fc) or framework region of an immunoglobulin or a fragment thereof to form a chimeric protein.
  • the fragment of the TNFR (TNFRI or TNFRII) polypeptide may be selected from one or more of SEQ ID NOs: 64, 66, 68, 92, 94, 96, 98.
  • the Fc region may be selected from the Fc region of the human isotypes of IgGl (for example, as substantially set forth in SEQ ID NO:2, SEQ ID NO:4), IgG2 (for example, as substantially set forth in SEQ ID NO: 6) IgG3 (for example, as substantially set forth in SEQ ID NO: 8), IgG4 (for example, as substantially set forth in SEQ ID NO: 10), IgAl (for example, as substantially set forth in SEQ ID NO: 12), IgA2 (for example, as substantially set forth in SEQ ID NO: 14), IgM (for example, as substantially set forth in SEQ ID NO: 16), IgE (for example, as substantially set forth in SEQ ID NO:18) or IgD (for example, as substantially set forth in SEQ ID NO: 20).
  • IgGl for example, as substantially set forth in SEQ ID NO:2, SEQ ID NO:4
  • IgG3 for example, as substantially set forth in SEQ ID NO: 8
  • the Fc receptor binding region or the complement activating region of the Fc region may be modified recombinantly, comprising one or more amino acid insertions, deletions or substitutions relative to the amino acid sequence of the Fc region.
  • the receptor binding region or the complement activating region of the Fc region may be modified chemically by changes to its glycosylation pattern, the addition or removal of carbohydrate moieties, the addition of polyunsaturated fatty acid moieties or other lipid based moieties to the amino acid backbone or to any associated co- or post-translational entities.
  • the Fc region may also be in a truncated form, resulting from the cleavage by an enzyme including papain, pepsin or any other site-specific proteases.
  • the Fc region may promote the spontaneous formation by the chimeric protein of a dimer, trimer or higher order multimer that is better capable of binding a TNF-a molecule and preventing it from binding to cell-bound receptors than the equivalent monomer. Therefore, the "TNFRI-Fc polypeptide" and "TNFRII-Fc polypeptide” contemplated by the present invention are antagonists of TNF-a activity.
  • TNF includes reference to TNF-a.
  • the present invention provides an isolated polypeptide encoded by a nucleotide sequence selected from the list consisting of SEQ ID NOs: 27, 29, 31, 33, 35,
  • nucleotide sequence having at least about 65% identity to any one of the above-listed sequence or a nucleotide sequence capable of hybridizing to any one of the above sequences or their complementary forms under low stringency conditions.
  • Another aspect of the present invention provides an isolated polypeptide encoded by a nucleotide sequence selected from the list consisting of SEQ ID NOs: 191, 192, 193 following splicing of their respective mRNA species by cellular processes.
  • Yet another aspect of the present invention provides an isolated polypeptide comprising an amino acid sequence selected from the list consisting of SEQ ID NOs: 28, 30, 32, 34, 36,
  • the present invention further contemplates a pharmaceutical composition
  • a pharmaceutical composition comprising at least part of the protein or chimeric molecule thereof, together with a pharmaceutically acceptable carrier, co-factor and/or diluent.
  • the present invention provides an isolated protein or chimeric molecule thereof, or a fragment thereof, encoded by a nucleotide sequence selected from the list consisting of SEQ ID NOs: 27, 29, 31, 33, 35, 37, 39, 43, 45, 47, 49, 51, 53, 55, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 127, 129, 131, 133, 135, 137, 139, 141, 143, 147, 149, 151, 153, 155,
  • nucleic acid molecule encoding protein or chimeric molecule thereof or a functional part thereof comprising a sequence of nucleotides having at least 60% similarity selected from the list consisting of SEQ ID NOs: 27, 29, 31, 33, 35, 37, 39, 43, 45, 47, 49, 51, 53, 55, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 127, 129, 131, 133, 135, 137, 139, 141, 143, 147, 149, 151, 153, 155, 157, 159, 163, 165, 167, 169, 171, 173, 175, 177, 179, 183, 185, 187,
  • the present invention is directed to an isolated nucleic acid molecule comprising a sequence of nucleotides encoding a protein or chimeric molecule in or related to the TNF superfamily, selected from the group comprising TNF-a, TNF-a-Fc, LT-a, LT-a-Fc, TNFRI, TNFRI-Fc, TNFRII, TNFRII-Fc, OX40, OX40-Fc, BAFF, BAFF- Fc, NGFR, NGFR-Fc, Fas Ligand, Fas Ligand-Fc, or a fragment thereof, an amino acid sequence substantially as set forth in one or more of SEQ ID NOs: 28, 30, 32, 34, 36, 38, 40, 44, 46, 48, 50, 52, 54, 56, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 90, 92, 94, 96, 98,
  • the present invention provides an isolated nucleic acid molecule encoding a protein or chimeric molecule in or related to the TNF superfamily, selected from the group comprising TNF-a-Fc, LT-a-Fc, TNFRI-Fc, TNFRII-Fc, OX40-Fc, BAFF- Fc, NGFR-Fc, Fas Ligand-Fc, or a fragment thereof, comprising a sequence of nucleotides selected from the group consisting of SEQ ID NOs: 31, 33, 35, 45, 47, 49, 51, 63, 65, 67, 91, 93, 95, 97, 129, 131, 151, 153, 155, 165, 167, 185, 187, linked directly or via one or more nucleotide sequences encoding protein linkers known in the art to nucleotide sequences encoding the constant (Fc) or framework region of a human immunoglobulin, substantially as set forth in one or more of S
  • the present invention provides an isolated protein in or related to the TNF superfamily, selected from the group comprising TNF-a-Fc, LT-a-Fc, TNFRI-Fc, TNFRII-Fc, OX40-Fc, BAFF-Fc, NGFR-Fc, Fas Ligand-Fc, or a fragment thereof, comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 32, 34, 36, 46, 48, 50, 52, 64, 66, 68, 92, 94, 96, 98, 130, 132, 152, 154, 156, 166, 168, 186, 188 linked directly or via one or more protein linkers known in the art, to the constant (Fc) or framework region of a human immunoglobulin, substantially as set forth in one or more of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18 or 20.
  • the present invention further extends to uses of an isolated protein or chimeric molecule thereof thereof or nucleic acid molecules encoding same in diagnostic, prophylactic, therapeutic, nutritional and/or research applications. More particularly, the present invention extends to a method of treating or preventing a condition or ameliorating the symptoms of a condition in an animal subject, said method comprising administering to said animal subject an effective amount of an isolated protein or chimeric molecule thereof.
  • the present invention provides a method for treating an inflammatory disease state which is characterized, exacerbated or otherwise associated with an excess of TNF -a in the subject, said method comprising administering to said subject a therapeutically effective amount of a pharmaceutical composition comprising TNFRI and/or TNFRII and/or a chimeric TNFRI or TNFRII molecule.
  • the disease state is selected from the list of: psoriasis, Behcet's disease, bullous dermatitis, eczema, fungal infection, leprosy, neutrophilic dermatitis, pityriasis maculara (or pityriasis rosea), pityriasis nigra (or tinea nigra), pityriasis rubra pilaris, systemic lupus erythematosus, systemic vascularitis and toxic epidermal necrolysis.
  • the disease state may be caused by the use of medication, for instance, the Aldara cream, including but not limited to erythema, erosion, ulceration, flaking, scaling, dryness, scabbing, crusting, weeping or exudating of skin.
  • the Aldara cream including but not limited to erythema, erosion, ulceration, flaking, scaling, dryness, scabbing, crusting, weeping or exudating of skin.
  • the present invention extends to uses of a protein or chimeric molecule thereof for screening small molecules, which may have a variety of diagnostic, prophylactic, therapeutic, nutritional and/or research applications.
  • the present invention further contemplates using an isolated protein or chimeric molecule thereof as immunogens to generate antibodies for therapeutic or diagnostic applications.
  • the present invention further contemplates using an isolated protein or chimeric molecule thereof in culture mediums for stem cells used in stem cell or related therapy.
  • the subject invention also provides a human derived protein or chimeric molecule thereof for use as a standard protein in an immunoassay and kits thereof.
  • the subject invention also extends to a method for determining the level of human cell-expressed human protein or chimeric molecule thereof in a biological preparation.
  • the subject invention also provides the use of a protein or chimeric molecule thereof in the manufacture of a formulation for diagnostic, prophylactic, therapeutic, nutritional and/or research applications.
  • the subject invention provides for a formulation suitable for topical application comprising a TNFRI and/or TNFRII and/or a chimeric TNFRI or TNFRII molecule comprising TNFRI or TNFRII fused directly or via one or more protein linkers to a Fc portion of an antibody or their functional homologs.
  • the topical application comprises one or more of TNFRI-Fc or TNFRII-Fc as described herein.
  • Figure 1 is a diagrammatic representation of the cloning process for inserting cDNA encoding a protein of the present invention into the pIRESbleo3 or pIRESbleo3-Fc vector.
  • Figure 2(a) shows a set of LC-MS chromatograms of N-glycans released from the
  • TNFRII-Fc of the present invention Top: Total Ion Chromatogram; Bottom: Base Peak Chromatogram.
  • Figure 2(b) shows a set of MS/MS spectra of the N-glycans present in the TNFRII-Fc of the present invention.
  • Figure 2(c) shows a set of LC-MS chromatograms of N-glycans released from TNFRII-Fc expressed in Chinese Hamster Ovary cells (Enbrel). Top: Total Ion Chromatogram; Bottom: Base Peak Chromatogram.
  • Figure 2(d) shows a set of MS/MS spectra of the N-glycans present in TNFRII-Fc expressed in Chinese Hamster Ovary cells.
  • Figure 2(e) shows a set of LC-MS chromatograms of O-glycans released from the TNFRII-Fc of the present invention. Top: Total Ion Chromatogram; Bottom: Base Peak Chromatogram.
  • Figure 2(f) shows a set of MS/MS spectra of the O-glycans present in the TNFRII-Fc of the present invention.
  • Figure 2(g) shows a set of LC-MS chromatograms of O-glycans released from TNFRII-Fc expressed in Chinese Hamster Ovary cells (Enbrel). Top: Total Ion Chromatogram; Bottom: Base Peak Chromatogram.
  • Figure 2(h) shows a set of MS/MS spectra of the O-glycans present in TNFRII-Fc expressed in Chinese Hamster Ovary cells.
  • Figure 3 (a) is a photograph of a hand of a patient suffering from pityriasis rubria pilaris prior to treatment. Note the redded skin and open lesions.
  • Figure 3(b) is a photograph of the same hand as shown in Figure 3 (a) two weeks after application of 2mL of a topical composition of the TNFRII-Fc of the present invention (250 ⁇ g/ml TNFRII-Fc; 20mg/ml thalidomide). Note the reduction of reddening and absence of lesions.
  • Figure 4 is a graph showing cell death of WEHI 164 cells treated with increasing concentrations of TNF -a of the present invention.
  • Figure 5 is a graph showing cell death of WEHI 164 cells treated with increasing concentrations of LT-a of the present invention.
  • Figure 6 is a graph showing the neutralizing ability of TNFRI-Fc of the present invention on the TNF-a mediated cytotoxicity of WEHI- 164 cells.
  • Figure 7 is a graph showing the neutralizing ability of TNFRII-Fc of the present invention on the TNF-a mediated cytotoxicity of WEHI- 164 cells.
  • Figure 8 is a graph comparing the inhibitory effect of TNFRII-Fc of the present invention (crosses) and TNFRII-Fc expressed in non-human cells (diamonds) on the TNF-a mediated cytotoxicity of murine L-929 cells.
  • Figure 9 is a graph comparing the proliferation of RPMI 8226 cells by BAFF of the present invention (filled circles) and human BAFF expressed using non-human cells (open circles).
  • Figure 10 is a graph showing the neutralizing ability of NGFR-Fc of the present invention on the NGF -beta induced proliferation of TF-I cells.
  • Figure 11 represents the in vitro comparison of immunoreactivity profiles between TNF-a of the present invention (squares) and human TNF-a expressed in E. coli cells (horizontal lines, R&D Systems; triangles WHO). ELISA kit standard curve (circles).
  • Figure 12 represents the in vitro comparison of immunoreactivity profiles between LT-a of the present invention (squares) and human LT-a expressed in E. coli cells (diamonds).
  • Figure 13 is a graph showing the biodistribution of TNFRII-Fc in mice following transdermal application of TNFRII-Fc in a topical formulation of the present invention.
  • compound used interchangeably herein to refer to a chemical compound and in particular a protein or chimeric molecule thereof that induces a desired pharmacological and/or physiological effect.
  • the terms also encompass pharmaceutically acceptable and pharmacologically active ingredients of those active agents specifically mentioned herein including but not limited to salts, esters, amides, prodrugs, active metabolites, analogs and the like.
  • references to a "compound”, “active agent”, “chemical agent” “pharmacologically active agent”, “medicament”, “active” and “drug” includes combinations of two or more actives such as two or more cytokines.
  • a “combination” also includes multi-part such as a two- part composition where the agents are provided separately and given or dispensed separately or admixed together prior to dispensation.
  • a multi-part pharmaceutical pack may have two or more proteins or chimeric molecules in or related to the TNF superfamily, selected from the group comprising TNF- a, TNF-a-Fc, LT-a, LT-a-Fc, TNFRI, TNFRI-Fc, TNFRII, TNFRII-Fc, OX40, OX40-Fc, BAFF, BAFF-Fc, NGFR, NGFR-Fc, Fas Ligand, Fas Ligand-Fc separately maintained.
  • an agent as used herein mean a sufficient amount of the protein or chimeric molecule thereof, alone or in combination with other agents to provide the desired therapeutic or physiological effect or outcome.
  • Undesirable effects e.g. side effects, are sometimes manifested along with the desired therapeutic effect; hence, a practitioner balances the potential benefits against the potential risks in determining what is an appropriate “effective amount”.
  • the exact amount required will vary from subject to subject, depending on the species, age and general condition of the subject, mode of administration and the like. Thus, it may not be possible to specify an exact "effective amount”. However, an appropriate "effective amount” in any individual case may be determined by one of ordinary skill in the art using only routine experimentation.
  • pharmaceutically acceptable carrier excipient or diluent
  • a pharmaceutical vehicle comprised of a material that is not biologically or otherwise undesirable, i.e. the material may be administered to a subject along with the selected active agent without causing any or a substantial adverse reaction.
  • Carriers may include excipients and other additives such as diluents, detergents, coloring agents, wetting or emulsifying agents, pH buffering agents, preservatives, and the like.
  • a "pharmacologically acceptable" salt, ester, amide, prodrug or derivative of a compound as provided herein is a salt, ester, amide, prodrug or derivative that this not biologically or otherwise undesirable.
  • treating and “treatment” as used herein refer to reduction in severity and/or frequency of symptoms of the condition being treated, elimination of symptoms and/or underlying cause, prevention of the occurrence of symptoms of the condition and/or their underlying cause and improvement or remediation or amelioration of damage following a condition.
  • Treating" a subject may involve prevention of a condition or other adverse physiological event in a susceptible individual as well as treatment of a clinically symptomatic individual by ameliorating the symptoms of the condition.
  • a "subject” as used herein refers to an animal, in a particular embodiment, a mammal and in a further embodiment human who can benefit from the pharmaceutical formulations and methods of the present invention. There is no limitation on the type of animal that could benefit from the presently described pharmaceutical formulations and methods. A subject regardless of whether a human or non-human animal may be referred to as an individual, patient, animal, host or recipient.
  • the compounds and methods of the present invention have applications in human medicine, veterinary medicine as well as in general, domestic or wild animal husbandry.
  • the animals are humans or other primates such as orangutans, gorillas, marmosets, livestock animals, laboratory test animals, companion animals or captive wild animals, as well as avian species.
  • laboratory test animals include mice, rats, rabbits, guinea pigs and hamsters. Rabbits and rodent animals, such as rats and mice, provide a convenient test system or animal model. Livestock animals include sheep, cows, pigs, goats, horses and donkeys. Non-mammalian animals such as avian species, fish, and amphibians including Xenopus spp prokaryotes and non-mammalian eukaryotes.
  • cytokine is used in its most general sense and includes any of various proteins secreted by cells to regulate the immune system, modulate the functional activities of individual cells and/or tissues, and/or induce a range of physiological responses.
  • cytokine should be understood to refer to a "complete” cytokine as well as fragments, derivatives or homologs or chimeras thereof comprising one or more amino acid additions, deletions or substitutions, but which substantially retain the biological activity of the complete cytokine.
  • cytokine receptor is a cell membrane associated or soluble portion of the cytokine receptor involved in cytokine signalling or regulation.
  • cytokine receptor should be understood to refer to a "complete” cytokine receptor as well as fragments, derivatives or homologs or chimeras thereof comprising one or more amino acid additions, deletions or substitutions, but which substantially retain the biological activity of the complete cytokine receptor.
  • protein is used in its most general sense and includes cytokines and cytokine receptors. As used herein, the term “protein” should be understood to refer to a "complete” protein as well as fragments, derivatives or homologs or chimeras thereof comprising one or more amino acid additions, deletions or substitutions, but which substantially retain the biological activity of the complete protein.
  • polypeptide refers to a polymer of amino acids and its equivalent but does not imply a limitation as to a specific length of the product, thus, peptides, oligopeptides, polypeptides and proteins are included within the definition of a "polypeptide". This term also includes all co- or post-translationally modified forms of a polypeptide. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid including, for example, unnatural amino acids such as those given in Table 5(a) or polypeptides with substituted linkages.
  • the present invention contemplates an isolated protein or chimeric molecule thereof having a profile of measurable physiochemical parameters (P x ), wherein the profile is indicative of, associated with or forms the basis of one or more distinctive pharmacological traits (Ty).
  • the isolated protein or chimeric molecule is a protein in or related to the TNF superfamily, selected from the group comprising TNF-a, TNF-a-Fc, LT-a, LT-a-Fc, TNFRI, TNFRI-Fc, TNFRII, TNFRII-Fc, OX40, OX40-Fc, BAFF, BAFF-Fc, NGFR, NGFR-Fc, Fas Ligand, Fas Ligand-Fc.
  • TNF-a, TNF-a-Fc, LT-a, LT-a-Fc, TNFRI, TNFRI-Fc, TNFRII, TNFRII-Fc, OX40, OX40-Fc, BAFF, BAFF-Fc, NGFR, NGFR-Fc, Fas Ligand, Fas Ligand-Fc includes reference to the whole polypeptide as well as fragments thereof.
  • the present invention provides an isolated protein or chimeric molecule thereof having a physiochemical profile comprising an array of measurable physiochemical parameters, ([P x ] 1 , [P x ] 2 ,...[P x ]n, ⁇ , wherein P x represents a measurable physiochemical parameter and "n" is an integer >1, wherein each of [P x ] 1 to [P x ] n is a different measurable physiochemical parameter, wherein the value of any one or more of the measurable physiochemical characteristics is indicative of, associated with, or forms the basis of, a distinctive pharmacological trait, T y , or a number of distinctive pharmacological traits ([T y ] 1 , [T y ] 2 , .
  • T y represents a distinctive pharmacological trait and m is an integer >1 and each of [T y ] 1 to [T y ] m is a different pharmacological trait.
  • measurable physiochemical parameters refers to one or more measurable characteristics of an isolated protein or chimeric molecule thereof.
  • exemplary "distinctive measurable physiochemical parameters” include, but are not limited to apparent molecular weight (P 1 ), isoelectric point (pi) (P 2 ), number of isoforms (P 3 ), relative intensities of the different number of isoforms (P 4 ), percentage by weight carbohydrate (P 5 ), observed molecular weight following N-linked oligosaccharide deglycosylation (P 6 ), observed molecular weight following N-linked and O-lmked oligosaccharide deglycosylation (P 7 ), percentage acidic monosaccharide content (Ps), monosaccharide content (P 9 ), sialic acid content (P 10 ), sulfate and phosphate content (P 11 ), Ser/Thr: GaINAc ratio (P 12 ), neutral percentage of N-linked oligosaccharide
  • pharmacological traits which in no way limit the invention include: therapeutic efficiency (T 1 ), effective therapeutic dose (TCID 5 o) (T 2 ), bioavailability (T 3 ), time between dosages to maintain therapeutic levels (T 4 ), rate of absorption (T 5 ), rate of excretion (T 6 ), specific activity (T 7 ), thermal stability (T 8 ), lyophilization stability (T 9 ), serum/plasma stability (T 10 ), serum half-life (T 11 ), solubility in blood stream (T 12 ), immunoreactivity profile (T 13 ), immunogenicity (T 14 ), inhibition by neutralizing antibodies (T 14A ), side effects (T 15 ), receptor/ligand binding affinity (T 16 ), receptor/ligand activation (T 17 ), tissue or cell type specificity (T 18 ), ability to cross biological
  • T 19 gut, lung, blood brain barriers, skin etc
  • T 19 angiogenic ability
  • T ⁇ A tissue uptake
  • T 2 o tissue uptake
  • T 21 stability to degradation
  • T 22 stability to freeze-thaw
  • T 23 stability to proteases
  • T 24 ease of administration
  • T 25 ease of administration
  • T 26 compatibility with other pharmaceutical excipients or carriers
  • T 28 persistence in organism or environment
  • T 29 stability in storage
  • T 30 toxicity in an organism or environment and the like
  • the protein or chimeric molecule of the present invention may have altered biological effects on different cells types (T 31 ), including but not limited to human primary cells, such as lymphocytes, erythrocytes, retinal cells, hepatocytes, neurons, keratinocytes, endothelial cells, endodermal cells, ectodermal cells, mesodermal cells, epithelial cells, kidney cells, liver cells, bone cells, bone marrow cells, lymph node cells, dermal cells, fibroblasts, T-cells, B-cells, plasma cells, natural killer cells, macrophages, neutrophils, granulocytes Langerhans cells, dendritic cells, eosinophils, basophils, mammary cells, lobule cells, prostate cells, lung cells, oesophageal cells, pancreatic cells, Beta cells (insulin secreting cells), hemangioblasts, muscle cells, oval cells (hepatocytes), mesenchymal cells, brain microvessel
  • the biological effects on the cells include effects on proliferation (T 32 ), differentiation (T 33 ), apoptosis (T 34 ), growth in cell size (T 35 ), cytokine adhesion (T 36 ), cell adhesion (T 37 ), cell spreading (T 38 ), cell motility (T 39 ), migration and invasion (T 40 ), chemotaxis (T 41 ), cell engulfment (T 42 ), signal transduction (T 43 ), recruitment of proteins to receptors/ligands (T 44 ), activation of the JAK/STAT pathway (T 45 ), activation of the Ras-erk pathway (T 46 ), activation of the AKT pathway (T 47 ), activation of the PKC pathway (T 48 ), activation of the PKA pathway (T 49 ), activation of src (T 50 ), activation of fas (T 51 ), activation of TNFR (T 52 ), activation of NFkB (T 53 ), activation of p38MAPK (T 54 ),
  • the term "distinctive" with regard to a pharmacological trait of a protein or a chimeric molecule of the present invention refers to one or more pharmacological traits of the protein or chimeric molecule thereof, which are distinctive for the particular physiochemical profile.
  • one or more of the pharmacological traits of the isolated protein or chimeric molecule thereof is different from, or distinctive relative to a form of the same protein or chimeric molecule produced in a prokaryotic or lower eukaryotic cell or even a higher non-human eukaryotic cell.
  • the pharmacological traits of the subject isolated protein or chimeric molecule thereof are substantially similar to or functionally equivalent to a naturally occurring protein.
  • prokaryote refers to any prokaryotic cell, which includes any bacterial cell (including actinobacterial cells) or archaeal cell.
  • non-mammalian eukaryote as used herein is self-evident. However, for clarity, this term specifically includes any non-mammalian eukaryote including: yeasts such as Saccharomyces spp. or Pichea spp.; other fungi; insects, including Drosophila spp. and insect cell cultures; fish, including Danio spp.; amphibians, including Xenopus spp.; plants and plant cell cultures.
  • stem cell includes embryonic or adult stem cells and includes those stem cells listed in Table 6.
  • a protein or chimeric molecule of the present invention may be used alone or in a cocktail of proteins to induce one or more of stem cell proliferation, differentiation or self-renewal.
  • Secondary structure of a protein or chimeric molecule thereof may be measured as an amino acid sequence.
  • Secondary structure may be measured as the number and/or relative position of one or more protein secondary structures such as ⁇ -helices, parallel ⁇ -sheets, antiparallel ⁇ -sheets or turns.
  • Tertiary structure describes the folding of the polypeptide chain to assemble the different secondary structure elements in a particular arrangement. As helices and sheets are units of secondary structure, so the domain is the unit of tertiary structure. In multi-domain proteins, tertiary structure includes the arrangement of domains relative to each other. Accordingly, tertiary structure may be measured as the presence, absence, number and/or relative position of one or more protein "domains".
  • Exemplary domains which in no way limit the present invention include: lone helices, helix-turn-helix domains, four helix bundles, DNA binding domains, three helix bundles, Greek key helix bundles, helix-helix packing domains, ⁇ -sandwiches, aligned ⁇ -sandwiches, orthogonal ⁇ - sandwiches, ⁇ -barrels, up and down antiparallel ⁇ -sheets, Greek key topology domains, jellyroll topology domains, ⁇ -propellers, ⁇ -trefoils, ⁇ -Helices, Rossman folds, ⁇ / ⁇ horseshoes, ⁇ / ⁇ barrels, ⁇ + ⁇ topologies, disulphide rich folds, serine proteinase inhibitor domains, sea anemone toxin domains, EGF-like domains, complement C-module domain, wheat plant toxin domains, Naja (Cobra) neurotoxin domains, green mamba anticho
  • Quaternary structure is described as the arrangement of different polypeptide chains within the protein structure, with each chain possessing individual primary, secondary and tertiary structure elements. Examples include either homo- or hetro- oligomeric multimerization (e.g. dimerization or trimerization).
  • the present invention provides an isolated protein or chimeric molecule thereof, or a fragment thereof, encoded by a nucleotide sequence selected from the list consisting of SEQ ID NOs: 27, 29, 31, 33, 35, 37, 39, 43, 45, 47, 49, 51, 53, 55, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 127, 129, 131, 133, 135, 137, 139, 141, 143, 147, 149, 151, 153, 155, 157, 159, 163, 165, 167, 169, 171, 173, 175, 177, 179, 183, 185, 187, 189, or a nucleotide sequence
  • Another aspect of the present invention provides an isolated polypeptide encoded by a nucleotide sequence selected from the list consisting of SEQ ID NOs: 191, 192, 193 following splicing of their respective mRNA species by cellular processes.
  • nucleic acid molecule encoding protein or chimeric molecule thereof or a functional part thereof comprising a sequence of nucleotides having at least 60% similarity selected from the list consisting of SEQ ID NOs: 27, 29, 31, 33, 35, 37, 39, 43, 45, 47, 49, 51, 53, 55, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 127, 129, 131, 133, 135, 137, 139, 141, 143, 147, 149, 151, 153, 155, 157, 159, 163, 165, 167, 169, 171, 173, 175, 177, 179, 183, 185, 187,
  • the present invention is directed to an isolated nucleic acid molecule comprising a sequence of nucleotides encoding a protein or chimeric molecule thereof, or a fragment thereof, an amino acid sequence substantially as set forth in one or more of SEQ ID NOs: 28, 30, 32, 34, 36, 38, 40, 44, 46, 48, 50, 52, 54, 56, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 128, 130, 132, 134, 136, 138, 140, 142, 144, 148, 150, 152, 154, 156, 158, 160, 164, 166, 168, 170, 172, 174, 176, 178, 180, 184, 186,
  • the present invention provides an isolated nucleic acid molecule encoding a protein molecule, or a fragment thereof, comprising a sequence of nucleotides selected from the group consisting of SEQ ID NOs: 31, 33, 35, 45, 47, 49, 51, 63, 65, 67, 91, 93, 95, 97, 129, 131, 151, 153, 155, 165, 167, 185, 187, linked directly or via one or more nucleotide sequences encoding protein linkers known in the art to nucleotide sequences encoding the constant (Fc) or framework region of a human immunoglobulin, substantially as set forth in one or more of SEQ ID NOs: 1, 3, 5, 7, 9, 11, 13, 15, 17 or 19.
  • the nucleotide sequences encoding protein linker comprises nucleotide sequences selected from IP, GSSNT, TRA or VDGIQWIP.
  • the present invention provides an isolated protein molecule, or a fragment thereof, comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 32, 34, 36, 46, 48, 50, 52, 64, 66, 68, 92, 94, 96, 98, 130, 132, 152, 154, 156, 166, 168, 186, 188 linked directly or via one or more protein linkers known in the art, to the constant (Fc) or framework region of a human immunoglobulin, substantially as set forth in one or more of SEQ ID NOs: 2, 4, 6, 8, 10, 12, 14, 16, 18 or 20.
  • Another aspect of the present invention provides an isolated protein or chimeric molecule thereof, or a fragment thereof, comprising an amino acid sequence selected from the list consisting of SEQ ID NOs: 28, 30, 32, 34, 36, 38, 40, 44, 46, 48, 50, 52, 54, 56, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 128, 130, 132, 134, 136, 138, 140, 142, 144, 148, 150, 152, 154, 156, 158, 160, 164, 166, 168, 170, 172, 174, 176, 178, 180, 184, 186, 188, 190, or an amino acid sequence having at least about 65% similarity to one or more of the above sequence
  • percentage amino acid similarity or nucleotide identity levels include at least about 61% or at least about 62% or at least about 63% or at least about
  • a “derivative" of a polypeptide of the present invention also encompasses a portion or a part of a full-length parent polypeptide, which retains partial transcriptional activity of the parent polypeptide and includes a variant.
  • Such "biologically-active fragments” include deletion mutants and small peptides, for example, for at least 10, in a particular embodiment, at least 20 and in a further embodiment at least 30 contiguous amino acids, which exhibit the requisite activity.
  • Peptides of this type may be obtained through the application of standard recombinant nucleic acid techniques or synthesized using conventional liquid or solid phase synthesis techniques.
  • peptides can be produced by digestion of an amino acid sequence of the invention with proteinases such as endoLys-C, endoArg-C, endoGlu-C and staphylococcus V8-protease.
  • the digested fragments can be purified by, for example, high performance liquid chromatographic (HPLC) techniques. Any such fragment, irrespective of its means of generation, is to be understood as being encompassed by the term "derivative" as used herein.
  • nucleotide sequence refers, therefore, to nucleotide sequences displaying substantial sequence identity with reference nucleotide sequences or polynucleotides that hybridize with a reference sequence under stringency conditions that are defined hereinafter.
  • nucleotide sequence refers, therefore, to nucleotide sequences displaying substantial sequence identity with reference nucleotide sequences or polynucleotides that hybridize with a reference sequence under stringency conditions that are defined hereinafter.
  • nucleotide sequence polynucleotide
  • nucleic acid molecule may be used herein interchangeably and encompass polynucleotides in which one or more nucleotides have been added or deleted, or replaced with different nucleotides.
  • the nucleic acid molecules of the present invention may be in the form of a vector or other nucleic acid construct.
  • the vector is DNA and may optionally comprise a selectable marker.
  • selectable markers include genes conferring resistance to compounds such as antibiotics, genes conferring the ability to grow on selected substrates, genes encoding proteins that produce detectable signals such as luminescence.
  • antibiotic resistance genes such as the neomycin resistance gene (neo) and the hygromycin resistance gene (hyg).
  • Selectable markers also include genes conferring the ability to grown on certain media substrates such as the tk gene (thymidine kinase) or the hprt gene (hypoxanthine phosphoribosyltransferase) which confer the ability to grow on HAT medium (hypoxanthine, aminopterin and thymidine); and the bacterial gpt gene (guanine/xanthine phosphoribosyltransferase) which allows growth on MAX medium (mycophenolic acid, adenine and xanthine).
  • Other selectable markers for use in mammalian cells and plasmids carrying a variety of selectable markers are described in Sambrook et al. Molecular Cloning - A Laboratory Manual, Cold Spring Harbour, New York, USA, 1990.
  • the selectable marker may depend on its own promoter for expression and the marker gene may be derived from a very different organism than the organism being targeted (e.g. prokaryotic marker genes used in targeting mammalian cells). However, it is favorable to replace the original promoter with transcriptional machinery known to function in the recipient cells. A large number of transcriptional initiation regions are available for such purposes including, for example, metallothionein promoters, thymidine kinase promoters, ⁇ -actin promoters, immunoglobulin promoters, SV40 promoters and human cytomegalovirus promoters.
  • a widely used example is the ⁇ pSV2-neo plasmid which has the bacterial neomycin phosphotransferase gene under control of the S V40 early promoter and confers in mammalian cells resistance to G418 (an antibiotic related to neomycin).
  • G418 an antibiotic related to neomycin.
  • a number of other variations may be employed to enhance expression of the selectable markers in animal cells, such as the addition of a poly(A) sequence and the addition of synthetic translation initiation sequences. Both constitutive and inducible promoters may be used.
  • the genetic construct of the present invention may also comprise a 3' non-translated sequence.
  • a 3 1 non-translated sequence refers to that portion of a gene comprising a DNA segment that contains a polyadenylation signal and any other regulatory signals capable of affecting mRNA processing or gene expression.
  • the polyadenylation signal is characterized by affecting the addition of polyadenylic acid tracts to the 3' end of the mRNA precursor.
  • Polyadenylation signals are commonly recognized by the presence of homology to the canonical form 5' AATAAA-3' although variations are not uncommon.
  • a genetic construct comprising a nucleic acid molecule of the present invention, operably linked to a promoter, may be cloned into a suitable vector for delivery to a cell or tissue in which regulation is faulty, malfunctioning or non-existent, in order to rectify and/or provide the appropriate regulation.
  • Vectors comprising appropriate genetic constructs may be delivered into target eukaryotic cells by a number of different means well known to those skilled in the art of molecular biology.
  • similarity includes exact identity between compared sequences at the nucleotide or amino acid level. Where there is non-identity at the nucleotide level, “similarity” includes differences between sequences which result in different amino acids that are nevertheless related to each other at the structural, functional, biochemical and/or conformational levels. Where there is non-identity at the amino acid level, “similarity” includes amino acids that are nevertheless related to each other at the structural, functional, biochemical and/or conformational levels. This includes “conserved” amino acid residues which are equivalent on the basis of polarity and/or charge. Table 5(b) displays the amino acids that are "equivalent” on the basis of polarity and/or charge. In a particular embodiment, nucleotide and sequence comparisons are made at the level of identity rather than similarity.
  • references to describe sequence relationships between two or more polynucleotides or polypeptides include “reference sequence”, “comparison window”, “sequence similarity”, “sequence identity”, “percentage of sequence similarity”, “percentage of sequence identity”, “substantially similar” and “substantial identity”.
  • a “reference sequence” is at least 12 but frequently 15 to 18 and often at least 25 or above, such as 30 monomer units, inclusive of nucleotides and amino acid residues, in length. Because two polynucleotides may each comprise (1) a sequence (i.e.
  • sequence comparisons between two (or more) polynucleotides are typically performed by comparing sequences of the two polynucleotides over a "comparison window" to identify and compare local regions of sequence similarity.
  • a “comparison window” refers to a conceptual segment of typically 12 contiguous residues that is compared to a reference sequence.
  • the comparison window may comprise additions or deletions (i.e. gaps) of about 20% or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences.
  • Optimal alignment of sequences for aligning a comparison window may be conducted by computerized implementations of algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package Release 7.0, Genetics Computer Group, 575 Science Drive Madison, WI, USA) or by inspection and the best alignment (i.e. resulting in the highest percentage homology over the comparison window) generated by any of the various methods selected.
  • GAP Garnier et al.
  • Altschul et al. Nucl Acids Res 25:389, 1997.
  • a detailed discussion of sequence analysis can be found in Unit 19.3 of Ausubel et al. ⁇ In: Current Protocols in Molecular Biology, John Wiley & Sons Inc. 1994- 1998).
  • sequence similarity and “sequence identity” as used herein refers to the extent that sequences are identical or functionally or structurally similar on a nucleotide-by- nucleotide basis or an amino acid-by-amino acid basis over a window of comparison.
  • a “percentage of sequence identity” is calculated by comparing two optimally aligned sequences over the window of comparison, determining the number of positions at which the identical nucleic acid base (e.g. A, T, C, G, I) or the identical amino acid residue (e.g.
  • sequence identity will be understood to mean the "match percentage” calculated by the DNASIS computer program (Version 2.5 for windows; available from Hitachi Software Engineering Co., Ltd., South San Francisco, California, USA) using standard defaults as used in the reference manual accompanying the software.
  • low stringency includes and encompasses from at least about 0 to at least about 15% v/v formamide and from at least about 1 M to at least about 2 M salt for hybridization, and at least about 1 M to at least about 2 M salt for washing conditions.
  • low stringency is at from about 25-30°C to about 42°C, such as 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41 and 42°C.
  • the temperature may be altered and higher temperatures used to replace formamide and/or to give alternative stringency conditions.
  • Alternative stringency conditions may be applied where necessary, such as medium stringency, which includes and encompasses from at least about 16% v/v to at least about 30% v/v formamide, such as 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 and 30% and from at least about 0.5 M to at least about 0.9 M salt, such as 0.5, 0.6, 0.7, 0.8 or 0.9 M for hybridization, and at least about 0.5 M to at least about 0.9 M salt, such as 0.5, 0.6, 0.7, 0.8 or 0.9 M for washing conditions, or high stringency, which includes and encompasses from at least about 31% v/v to at least about 50% v/v formamide, such as 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49 and 50% and from at least about 0.01 M to at least about 0.15 M salt, such as 0.01, 0.02, 0.03, 0.04, 0.05, 0.06, 0.07, 0.08, 0.
  • T m 69.3 + 0.41 (G+C)% (Marmur and Doty, J MoI Biol 5:109, 1962).
  • T m of a duplex DNA decreases by I°C with every increase of 1% in the number of mismatch base pairs (Bonner and Laskey, Eur J Biochem 46:83, 191 A.
  • Formamide is optional in these hybridization conditions.
  • levels of stringency are defined as follows: low stringency is 6 x SSC buffer, 0.1% w/v SDS at 25-42°C; a moderate stringency is 2 x SSC buffer, 0.1% w/v SDS at a temperature in the range 20°C to 65°C; high stringency is 0.1 x SSC buffer, 0.1% w/v SDS at a temperature of at least 65°C.
  • co- or post-translational modifications refer to covalent modifications occurred during or after translation of the peptide chain.
  • exemplary co- or post-translational modifications include but are not limited to acylation (including acetylation), amidation or deamidation, biotinylation, carbamylation (or carbamoylation), carboxylation or decarboxylation, disulfide bond formation, fatty acid acylation (including myristoylation, palmitoylation and stearoylation), formylation, glycation, glycosylation, hydroxylation, incorporation of selenocysteine, lipidation, lipoic acid addition, methylation, N- or C-terminal blocking, N- or C-terminal removal, nitration, oxidation of methionine, phosphorylation, proteolytic cleavage, prenylation (including faraesylation, geranyl geranylation), pyridoxal phosphate addition, sialylation
  • Acetyl Co-A is the acetyl donor for acylation.
  • Amidation is the covalent linkage of an amide group to the carboxy terminus of a peptide and is frequently required for biological activity and stability of a protein. Deamidation is the hydrolytic removal of an amide group. Deamidation of amide containing amino acid residues is a rare modification that is performed by the organism to re-arrange the 3D structure and alter the charge ratio/pi.
  • Biotinylation is a technique whereby biotinyl groups are incorporated into molecules, either that catalyzed by holocarboxylase synthetase during enzyme biosynthesis or that undertaken in vitro to visualise specific substrates by incubating them with biotin-labeled probes and avidin or streptavidin that has been linked to any of a variety of substances amenable to biochemical assay.
  • Carbamylation is the transfer of the carbamoyl from a carbamoyl- containing molecule (e.g., carbamoyl phosphate) to an acceptor moiety such as an amino group.
  • Carboxylation of glutamic acid residues is a vitamin K dependent reaction that results in the formation of a gamma carboxyglutamic acid (GIa residue).
  • GIa residues within several proteins of the blood-clotting cascade are necessary for biological function of the proteins. Carboxylation can also occur to aspartic acid residues.
  • Disulfide bonds are covalent linkages that form when the thiol groups of two cysteine residues are oxidized to a disulfide. Many mammalian proteins contain disulfide bonds, and these are crucial for the creation and maintenance of tertiary structure of the protein, and thus biological activity.
  • Protein synthesis in bacteria involves formylation and deformylation of N-terminal methionines. This formylation/deformylation cycle does not occur in cytoplasm of eukaryotic cells and is a unique feature of bacterial cells. In addition to the hydroxylation that occurs on glycine residues as part of the amidation process, hydroxylation can also occur in proline and lysine residues catalysed by prolyl and lysyl hydroxylase (Kivirikko et al. FASEB Journal 3: 1609- 1617, 1989).
  • Glycation is the uncontrolled, non-enzymatic addition of glucose or other sugars to the amino acid backbone of protein.
  • Glycosylation is the addition of sugar units to the polypeptide backbone and is further described hereinafter.
  • Hydroxylation is a reaction which is dependent on vitamin C as a co-factor. Adding to the importance of hydroxylation as a post- translation modification is that hydroxy-lysine serves as an attachment site for glycosylation.
  • Selenoproteins are proteins which contain selenium as a trace element by the incorporation of a unique amino acid, selenocysteine, during translation.
  • the tRNA for selenocysteine is charged with serine and then enzymatically selenylated to produce the selenocysteinyl- tRNA.
  • the anticodon of selenocysteinyl-tRNA interacts with a stop codon in mRNA
  • UGA 3' non-translated region
  • Fatty acid acylation involves the covalent attachment of fatty acids such as the 14 carbon Myristic acid (Myristoylation), the 16 carbon Palmitic acid (Palmitoylation) and the 18 carbon Stearic acid (Stearoylation). Fatty acids are linked to proteins in the pre-Golgi compartment and may regulate the targeting of proteins to membranes (Blenis and Resh Curr Opin Cell Biol 5(6):984-9, 1993). Fatty acid acylation is, therefore, important in the functional activity of a protein (Bernstein Methods MoI Biol 237:195-204, 2004).
  • Prenylation involves the addition of prenyl groups, namely the 15 carbon farnesyl or the 20 carbon geranyl-geranyl group to acceptor proteins.
  • the isoprenoid compounds including farnesyl diphosphate or geranylgeranyl diphosphate, are derived from the cholesterol biosynthetic pathway.
  • the isoprenoid groups are attached by a thioether link to cysteine residues within the consensus sequence CAAX, (where A is any aliphatic amino acid, except alanine) located at the carboxy terminus of proteins.
  • Prenylation enhances proteins ability to associate with lipid membranes and all known GTP-binding and hydrolyzing proteins (G proteins) are modified in this way, making prenylation crucial for signal transduction. (Rando Biochim Biophys Acta 1300(l):5-l6, 1996; GeIb et al. Curr Opin Chem Biol 2(I):40-8, 1998).
  • Lipoic acid is a vitamin-like antioxidant that acts as a free radical scavenger.
  • Lipoyl-lysine is formed by attaching lipoic acid through an amide bond to lysine by lipoate protein ligase.
  • Protein methylation is a common modification that can regulate the activity of proteins or create new types of amino acids.
  • Protein methyltransferases transfer a methyl group from S-adenosyl-L-methionine to nucleophilic oxygen, nitrogen, or sulfur atoms on the protein.
  • the effects of methylation fall into two general categories. In the first, the relative levels of methyltransferases and methylesterases can control the extent of methylation at a particular carboxyl group, which in turn regulates the activity of the protein. This type of methylation is reversible.
  • the second group of protein methylation reactions involves the irreversible modification of sulfur or nitrogen atoms in the protein. These reactions generate new amino acids with altered biochemical properties that alter the activity of the protein (Clarke Curr Opin Cell Biol 5:977 983, 1993).
  • Protein nitration is a significant post-translational modification, which operates as a transducer of nitric oxide signalling. Nitration of proteins modulates catalytic activity, cell signalling and cytoskeletal organization.
  • Phosphorylation refers to the addition of a phosphate group by protein kinases. Serine, threonine and tyrosine residues are the amino acids subject to phosphorylation. Phosphorylation is a critical mechanism, which regulates biological activity of a protein.
  • proteins are also modified by proteolytic cleavage. This may simply involve the removal of the initiation methionine.
  • Other proteins are synthesized as inactive precursors (proproteins) that are activated by limited or specific proteolysis. Proteins destined for secretion or association with membranes (preproteins) are synthesized with a signal sequence of 12-36 predominantly hydrophobic amino acids, which is cleaved following passage through the ER membrane.
  • Pyridoxal phosphate is a co-enzyme derivative of vitamin B6 and participates in transaminations, decarboxylations, racemizations, and numerous modifications of amino acid side chains.
  • AU pyridoxal phosphate-requiring enzymes act via the formation of a Schiff base between the amino acid and coenzyme.
  • Most enzymes responsible for attaching the pyridoxal-phosphate group to the lysine residue are self activating.
  • Sialylation refers to the attachment of sialic acid to the terminating positions of a glycoprotein via various sialyltransferase enzymes; and desialylation refers the removal of sialic acids.
  • Sialic acids include but are not limited to, N-acetyl neuraminic acid (NeuAc) and N-glycolyl neuraminic acid (NeuGc).
  • Sialyl structures that result from the sialylation of glycoproteins include sialyl Lewis structures, for example, sialyl Lewis a and sialyl Lewis x, and sialyl T structures, for example, Sialyl-TF and Sialyl Tn.
  • Sulfation occurs at tyrosine residues and is catalyzed by the enzyme tyrosylprotein sulfotransferase which occurs in the trans-Golgi network. It has been determined that 1 in 20 of the proteins secreted by HepG2 cells and 1 in 3 of those secreted by fibroblasts contain at least one tyrosine sulfate residue. Sulfation has been shown to influence biological activity of proteins.
  • CCR5 a major HIV co- receptor
  • sulfation of one or more tyrosine residues in the N-terminal extracellular domain of CCR5 are required for optimal binding of MIP-I alpha/CCL3, MIP-I beta/CCL4, and RANTES/CCL5 and for optimal HIV co- receptor function (Moore J Biol Chem 278(27) /24243 -24246, 2003). Sulfation can also occur on sugars.
  • glycosulfation of a carbohydrate moiety of a glycoprotein can occur by the action of glycosulfotransferases such as GalNAc( ⁇ l-4)GlcNAc( ⁇ l-2)Man ⁇ 4 sulfotransferase.
  • Ubiquitin is a 76 amino acid protein which both self associates and covalently attaches to other proteins in mammalian cells. The attachment is via a peptide bond between the C-terminus of ubiquitin and the amino group of lysine residues in other proteins. Attachment of a chain of ubiquitin molecules to a protein targets it for proteolysis by the proteasome and is an important mechanism for regulating the steady state levels of regulatory proteins e.g. with respect to the cell cycle (Wilkinson Annu Rev Nutr /5:161-89, 1995). In contrast, mono- ubiquitination can play a role in direct regulation of protein function. Ubiquitin-like proteins that can also be attached covalently to proteins to influence their function and turnover include NEDD-8, SUMO-I and A ⁇ gl2.
  • sugar residues in the polypeptide backbone include but are not limited to: fucose (Fuc), galactose (Gal), glucose (GIc), galactosamine (GaINAc), glucosamine (GIcNAc), mannose (Man), N-acetyl-lactosamine (lacNAc) N,N'- diacetyllactosediamine (lacdiNAc).
  • Fuc fucose
  • Gal galactose
  • GIc glucose
  • GaINAc galactosamine
  • GIcNAc glucosamine
  • Man mannose
  • lacNAc N-acetyl-lactosamine
  • lacdiNAc N,N'- diacetyllactosediamine
  • glycophosphatidylinositol anchor used to secure some proteins to cell membranes
  • the glycosylation structure can comprise one or more of the following carbohydrate antigenic determinants in Table 7.
  • the carbohydrates will also contain several antennary structures, including mono, bi, tri and tetra outer structures.
  • Glycosylation may be measured by the presence, absence or pattern of N-lmked glycosylation, O-linked glycosylation, C-linked mannose structure, and glycophosphatidylinositol anchor; the percentage of carbohydrate by mass; Ser/Thr - GaINAc ratio; the proportion of mono, bi, tri and tetra sugar structures or by lectin or antibody binding.
  • Sialylation of a protein may be measured by the immunoreactivity of the protein with an antibody directed against a particluar sialyl structure.
  • Lewis x specific antibodies react with CEACAMl expressed from granulocytes but not with recombinant human CEACAMl expressed in 293 cells (Lucka et al. Glycobiology 15(l):S7-l00, 2005).
  • the presence of sialylated structures on a protein may be detected by a combination of glycosidase treatment followed by a suitable measurement procedure such as mass spectroscopy (MS), high performance liquid chromatography (HPLC) or glyco mass fingerprinting (GMF).
  • MS mass spectroscopy
  • HPLC high performance liquid chromatography
  • GMF glyco mass fingerprinting
  • the apparent molecular weight of a protein includes all elements of a protein complex (cofactors and non-covalently bonded domains) and all co- or post-translational modifications (addition or removal of covalently bonded groups to and from peptide). Apparent molecular weight is often affected by co- or post-translational modifications.
  • a protein's apparent molecular weight may be determined by SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis), which is also the second dimension on its two- dimensional counterpart, 2D-P AGE (two-dimensional polyacrylamide gel electrophoresis).
  • MS mass spectrometry
  • MALDI-TOF Matrix-Assisted Laser Desorption Ionization - Time of Flight
  • ESI Electrospray Ionization
  • the isolated protein or chimeric molecule of the present invention has a apparent molecular weight of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110,
  • the isoelectric point (or pi) of a protein is the pH at which the protein carries no net charge. This attribute may be determined by isoelectric focusing (IEF), which is also the first dimension of 2D-P AGE. Experimentally determined pI values are affected by a range of co- or post-translational modifications and therefore the difference between an experimental pi and theoretical pi may be as high as 5 units. Accordingly, an isolated protein or chimeric molecule of the present invention may have a pi of 0, 1.0, 1.1, 1.2, 1.3,
  • the term “isoform” means multiple molecular forms of a given protein, and includes proteins differing at the level of (1) primary structure (such as due to alternate RNA splicing, or polymorphisms); (2) secondary structure (such as due to different co- or post translational modifications); and/or (3) tertiary or quaternary structure (such as due to different sub-unit interactions, homo- or hetero- oligomeric multimerization).
  • the term “isoform” includes glycoform, which encompasses a protein or chimeric molecule thereof having a constant primary structure but differing at the level of secondary or tertiary structure or co-or post-translational modification such as different glycosylation forms.
  • Chemical stability of a protein may be measured as the "half-life" of the protein in a particular solvent or environment.
  • proteins with a molecular weight of less than 50 kDa have a half-life of approximately 5 to 20 minutes.
  • the proteins or chimeric molecules of the present invention are contemplated to have a half-life of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89
  • the binding affinity of a protein or chimeric molecule thereof to its ligand or receptor may be measured as the equilibrium dissociation constant (Kd) or functionally equivalent measure.
  • the solubility of a protein may be measured as the amount of protein that is soluble in a given solvent and/or the rate at which the protein dissolves. Furthermore, the rate and or level of solubility of a protein or chimeric molecule thereof in solvents of differing properties such as polarity, pH, temperature and the like may also provide measurable physiochemical characteristics of the protein or chimeric molecule thereof.
  • measurable physiochemical parameters may be determined, measured, quantified or qualified using any methods known to one of skill in the art. Described below is a range of methodologies which may be useful in determining, measuring, quantifying or qualifying one or more measurable physiochemical parameters of an isolated protein or chimeric molecule thereof. However, it should be understood that the present invention is in no way limited to the particular methods described, or to the measurable physiochemical parameters that are measurable using these methods. Glycoproteins can be said to have two basic components that interact with each other to create the molecule as a whole- the amino acid sequence and the carbohydrate or sugar side chains.
  • the carbohydrate component of the molecule exists in the form of monosaccharide or oligosaccharide side chains attached to the amine side chain of Asn or the hydroxyl side chain of Ser/Thr residues of the amino acid backbone by N- or O- linkages, respectively.
  • a monosaccharide is the term given to the smallest unit of a carbohydrate that is regarded as a sugar, having the basic formula of (CH 2 O) n and most often forming a ring structure of 5 or 6 atoms (pentoses and hexoses respectively).
  • Oligosaccharides are combinations of monosaccharides forming structures of varying complexities that may be either linear or branched but which generally do not have long chains of tandem repeating units (such as is the case for polysaccharides).
  • the level of branching that the oligosaccharide contains as well as the terminal and branching substitutions dramatically affect the properties of the glycoprotein as a whole, and play an important role in the biological function of the molecule.
  • Oligosaccharides are manufactured and attached to the amino acid backbone in the endoplasmic reticulum (ER) and Golgi apparatus of the cell.
  • Glycan chains are often expressed in a branched fashion, and even when they are linear, such chains are often subject to various modifications.
  • complete sequencing of oligosaccharides is difficult to accomplish by a single method and therefore requires iterative combinations of physical and chemical approaches that eventually yield the details of the structure under study.
  • Determination of the glycosylation pattern of a protein can be performed using a number of different systems, for example using SDS-PAGE. This technique relies on the fact that glycosylated proteins often migrate as diffuse bands by SDS-PAGE. Differentiation between different isoforms are performed by treating a protein with a series of agents. For example, a marked decrease in band width and change in migration position after digestion with peptide-N4-(N-acetyl- ⁇ -D-glucosaminyl) asparagine amidase (PNGase) is considered diagnostic of N-linked glycosylation.
  • PNGase peptide-N4-(N-acetyl- ⁇ -D-glucosaminyl) asparagine amidase
  • N-linked oligosaccharides are removed from the protein with PNGase cloned from Flavobacterium meningosepticum and expressed in E. coli.
  • the removed N-linked oligosaccharides may be recovered from Alltech Carbograph SPE Carbon columns (Deerfield, Illinois, USA) as described by Packer et al Glycoconj J 5(8):737-47, 1998.
  • the sample can then be taken for monosaccharide analysis, sialic acid analysis or sulfate analysis on a Dionex system with a GP50 pump ED50 pulsed Amperometric or conductivity detector and a variety of pH anion exchange columns.
  • the extent of O-linked glycosylation may be determined by first removing O-linked oligosaccharides from the target protein by ⁇ -elimination.
  • the removed O-linked oligosaccharides may be recovered from Alltech Carbograph SPE Carbon columns (Deerfield, Illinois, USA) as described by Packer et al. (1998, supra).
  • the sample can then be taken for monosaccharide analysis, sialic acid analysis or sulfate analysis on a Dionex system with a GP50 pump ED50 pulsed Amperometric or conductivity detector and a variety of pH anion exchange columns.
  • Monosaccharide subunits of an oligosaccharide have variable sensitivities to acid and thus can be released from the target protein by mild trifluoro-acetic acid (TFA) conditions, moderate TFA conditions, and strong hydrochloric acid (HCl) conditions.
  • TFA trifluoro-acetic acid
  • HCl hydrochloric acid
  • the monosaccharide mixtures are then separated by high pH anion exchange chromatography (HPAEC) using a variety of column media, and detected using pulsed amperometric electrochemical detection (PAD).
  • HPAEC high pH anion exchange chromatography
  • High-pH anion-exchange chromatography with pulsed amperometric detection has been extensively used to determine monosaccharide composition. Fluorophore- based labeling methods have been introduced and many are available in kit form. A distinct advantage of fluorescent methods is an increase in sensitivity (about 50-fold).
  • One potential disadvantage is that different monosaccharides may demonstrate different selectivity for the fluorophore during the coupling reaction, either in the hydrolyzate or in the external standard mixture.
  • the increase in sensitivity and the ability to identify which monosaccharides are present from a small portion of the total amount of available glycoprotein, as well as the potential for greater sensitivity using laser-induced fluorescence makes this approach attractive.
  • a conductivity detector may be used to determine the sulfate and phosphate composition. By using standards, the peak areas can be calculated to total amounts of each monosaccharide present. These data can indicate the level of N- and O-linked glycosylation, the extent of sialylation, and in combination with amino acid composition, percent by weight glycosylation, percent by weight acidic glycoproteins.
  • PVDF Polysaccharide composition analysis of small amounts of protein is best performed with PVDF (PSQ) membranes, after electroblotting, or, if smaller aliquots are to be analyzed, on dot blots.
  • PVDF is an ideal matrix for carbohydrate analysis because neither monosaccharides nor oligosaccharides bind to the membrane, once released by acid or enzymatic hydrolysis.
  • Determination of the oligosaccharide content of the target molecule is performed by a number of techniques.
  • the sugars are first removed from the amino acid backbone by enzymatic (such as digestion with PNGase)) or chemical (such as beta elimination with hydroxide) means.
  • the sugars may be stabilised by reduction or labeled with a fluorophore for ease of detection.
  • the resultant free oligosaccharides are then separated either by high pH anion exchange chromatography with pulsed amperometric electrochemical detection (HPAEC-PAD), which can be used with known standards to determine the ratios of the various structures and levels of sialylation, or by fluorophore assisted carbohydrate electrophoresis (FACE) a process similar to SDS-PAGE separation of proteins.
  • HPAEC-PAD pulsed amperometric electrochemical detection
  • FACE fluorophore assisted carbohydrate electrophoresis
  • Fluorophore assisted carbohydrate electrophoresis is a polyacrylamide gel electrophoresis system designed to separate individual oligosaccharides that have been released from a glycoconjugate. Oligosaccharides are removed from the sample protein by either chemical or enzymatic means in such a way as to retain the reducing terminus. Oligosaccharides are then either digested into monosaccharides or left intact and labeled with a fluorophore (either charged or non charged). High percentage polyacrylamide gels and various buffer systems are used to migrate the oligosaccharides/monosaccharides which migrate relative to their size/composition in much the same way as proteins. Sugars are visualised by densitometry and relative amounts of sugars can be determined by fluorophore detection. This process is compatible with MALDI-TOF MS, hence the method can be used to elucidate actual structures.
  • Quartz crystal microbalance and surface plasmon resonance are two methods of obtaining biological information through the physiochemical properties of a molecule. Both measure protein-protein interactions indirectly through the change that the interaction causes in the physical characteristics of a prefabricated chip.
  • QCM a single crystal quartz wafer is treated with a receptor/antibody etc which interacts with the ligand of interest. This chip is oscillated by the microbalance and the frequency of the chip recorded.
  • the protein of interest is allowed to pass over the chip and the interaction with the bound molecule causes the frequency of the wafer to change. By changing the conditions by which the ligand interacts with the chip, it is possible to determine the binding characteristics of the target molecule.
  • Apparent molecular weight is also a physiochemical property which can be used to determine the similarities between the protein or chimeric molecule of the present invention and those produced using alternative means.
  • molecular weight is defined as the sum of atomic weights of the constituent atoms in a molecule, sometimes also referred to as “molecular mass” (Mr). Molecular weight can be determined theoretically by summing the atomic masses of the constituent atoms in a molecule.
  • apparent molecular weight is defined as the molecular weight determined by one or more analytical techniques such as SDS page or ultra centrifugation and depends on the relationship between the molecule and the detection system. The apparent molecular weight of a protein or chimeric molecule thereof can be determined using any one of a range of experimental methods.
  • Analytical methods for determining the molecular weight of a protein include, without being limited to, size- exclusion chromatography (SEC), gel electrophoresis, Rayleigh light scattering, analytical ultracentrifugation, and, to some extent, time-of-flight mass spectrometry.
  • SEC size- exclusion chromatography
  • gel electrophoresis gel electrophoresis
  • Rayleigh light scattering analytical ultracentrifugation
  • time-of-flight mass spectrometry time-of-flight mass spectrometry.
  • Gel electrophoresis is a process of determining some of the physiochemical properties (specifically apparent molecular weight and pi) of a protein and in the case of 2 dimensional electrophoresis to separate the molecule into isoforms, thereby providing information on the post-translational modifications of the protein product.
  • electrophoresis is the process of forcing a charged molecule (such as protein or DNA) to migrate through a gel matrix (most commonly polyacrylamide or agarose) by applying an electric potential through its body.
  • the most common forms of electrophoresis used on proteins are isoelectric focussing, native, and SDS polyacrylamide gel electrophoresis. In isoelectric focussing a protein is placed into a polyacrylamide gel that has a pH gradient across its length. The protein will migrate to the point in the gel where it has a net charge of zero thereby giving its isoelectric point.
  • Glyco mass fingerprinting is the process by which the oligosaccharide profile of a protein or one of its isoforms is identified by electrophoresis followed by specific mass spectrometric techniques.
  • Sample protein is purified either by ID SDS-PAGE for total profile determination or 2D gel electrophoresis for specific isoform characterization.
  • the protein band/spot is excised from the gel and de-stained to remove contaminants.
  • the sugars are released by chemical or enzymatic means and desalted/separated using a nanoflow LC system and a graphitised carbon column.
  • the LC flow can be directly injected into an electrospray mass spectrometer that is used to determine the mass and subsequently the identity of the oligosaccharides present on the sample. This provides a profile or fingerprint of each isoform which can be combined with quantitative techniques such as Dionex analysis to determine the total composition of the molecule being tested.
  • Primary structure can be evaluated in determining the physiochemical properties of the protein or chimeric molecule of the present invention.
  • the primary structure of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • Information on the primary structure of a protein or chimeric molecule thereof can be determined using a combination of mass spectrometry (MS), DNA sequencing, amino acid composition, protein sequencing and peptide mass fingerprinting.
  • MS mass spectrometry
  • N-terminal chemical sequencing utilises Edman chemistry (Ednian P. "Sequence determination" MoI Biol Biochem Biophys 5:211-55, 1970), which states that the peptide bond between the N-terminal amino acid and the amino acid in position 2 of the protein is weaker than all other peptide bonds in the sequence.
  • FTIC fluorophore
  • tandem mass spectrometry in conjunction with nanoflow liquid chromatography may be used (LC-MS/MS).
  • LC-MS/MS tandem mass spectrometry in conjunction with nanoflow liquid chromatography
  • the protein is digested into peptides using specific endoproteases and the molecular weight of the peptides determined.
  • High energy collision gases such as nitrogen or argon are then used to break the peptide bonds and the masses of the resultant peptides measured.
  • By calculating the change in mass of the peptides it is possible to determine the sequence of each of the peptides (each amino acid has a unique mass).
  • the peptides may then be overlapped to determine their order and thus the entire sequence of the protein.
  • Mass spectrometry is the process of measuring the mass of a molecule through extrapolation of its behavior in a charged environment under a vacuum. MS is very useful in stability studies and quality control. The method first requires digestion of samples by proteolytic enzymes (trypsin, V8 protease, chymotrypsin, subtilisin, and clostripain) (Franks et al. Characterization of proteins, Humana Press, Clifton, NJ, 1988; Hearn et al. Methods in Enzymol 104:190-212, 1984) and then separation of digested samples by reverse phase chromatography (RPC). With tryptic digestion in conjunction with LC-MS, the peptide map can be used to monitor the genetic stability, the homogeneity of production lots, and protein stability during fermentation, purification, dosage form manufacture and storage.
  • proteolytic enzymes trypsin, V8 protease, chymotrypsin, subtilisin, and clostripain
  • RPC reverse phase
  • HPLC/MS interface used in Caprioli's work used a fused silica capillary column to transport the eluate from the column to the tip of the sample probe in the ionization chamber of the mass spectrometer.
  • the probe tip is continuously bombarded with energetic Xe atoms, causing sputtering of the sample solution as it emerges from the tip of the capillary.
  • the mass is then analyzed by the instrument (Caprioli et al. Biochem Biophys Res Commun 146:291-299, 1987).
  • MS/MS and LC/MS interfaces expand the potential applications of MS.
  • MS/MS allows direct identification of partial to full sequence for peptides up to 25 AAs, sites of deamidation and isomerization (Carr et al. Anal Chem (55:2802-2824, 1991). Coupled with RPC or capillary electrophoresis (CE), MS can perform highly sensitive analysis of proteins (Figeys and Aebersold, Electrophoresis 19:885-892, 1998; Nguyen et al. J Chromatogr A 705:21-45, 1995).
  • LC/MS allows LC methodology to separate peptides before entering the MS, such as the continuous flow FAB interfaced with microbore HPLC (Caprioli et al.
  • Electrospray ionization MS uses an aerosol of solution protein to introduce into a needle under a high voltage, generating a series of charged peaks of the same molecules with various charges. Because each peak generated from the differently charged species produces an estimation of the molecular weights, these estimations can be combined to increase the overall precision of the molecular weight estimation.
  • Matrix Assisted Laser Desorption Ionization MS MALDI-MS uses a high concentration of a chromophore. A higher intensity laser pulse will be absorbed by the matrix and the energy absorbed evaporates part of the matrix and carries the protein sample with it into the vapor phase almost entirely. The resulting ions are then analyzed in a time of flight MS.
  • the mild ionization may enhance the capacity of the method to provide quaternary structure information.
  • MALDI-MS can be run rapidly in less than 15 minutes. It does not need to fragment the molecules and the result is easy to interpret as a densitometric scan of an SDS-PAGE gel, with a mass range up to over 10OkDa.
  • Amino acid sequence can be predicted by sequencing DNA that encodes a protein or chimeric molecule thereof. However, occasionally the actual protein sequence may be different. Traditionally, DNA sequencing reactions are just like the PCR reactions for replicating DNA (DNA denaturation, replication). By DNA cloning technology, the gene is cloned, and the nucleotide sequence determined.
  • amino acid sequence of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • Amino acid sequencing includes: in gel tryptic digestion, fractionation of the digested peptides by RPC-HPLC, screening the peptide peaks that have the most symmetrical absorbance profile by MALDI-TOF MS, and the first peptide (N- terminal) by Edman degradation. Ednian chemically derived primary sequence data is the classical method to identify proteins at the molecular level.
  • MALDI-TOF MS can be used for N-terminal sequence analysis.
  • all enzymatic digests for HPLC and peptide sequencing are recommended to first be subjected to MS or MS/MS protein identification to decrease the time and cost.
  • the internal amino acid sequences from SDS-P AGE- separated proteins are obtained by elution of the peptides with HPLC separation after an in situ tryptic or lysyl endopeptidase digestion in the gel matrix.
  • Edman degradation can be used for direct N-terminal sequencing with a chemical procedure, which derivatizes the N-terminal amino acids to release the amino acids and expose the amino terminal of the next AAs.
  • the Edman sequencing includes: 1).
  • microbore HPLC N-terminal sequence analysis is repeated by Edman chemistry cycles. Every cycle of the Edman chemistry can identify one amino acid. 2).
  • internal protein sequence analysis is conducted by Edman degradation chemistry.
  • Microbore HPLC and capillary HPLC are used for analysis and purification of peptide mixtures using RPC-HPLC. In-gel samples and PVDF samples are purified using different columns.
  • MALDI-TOF MS analysis can be used for N-terminal analysis after HPLC fractionation.
  • the selection criteria are: 1) The apparent purity of the HPLC fraction. 2) The mass and thus the estimated length of the peptide.
  • the peptide mass information is useful for confirming the Edman sequencing amino acid assignments, and also in the possible detection of co- or post-translational modifications.
  • In-gel digests are suitable for purification on the higher sensitivity HPLC system.
  • the internal protein sequence analysis is first enzymatically digested by SDS-PAGE. Proteins in an SDS-PAGE mini-gel can be reliably digested in-gel only with trypsin.
  • the peptide fragments are purified by RPC-HPLC and then analyzed by MALDI-TOF MS, screening for peptides suitable for Edman sequence analysis. Proteins in a gel can only be analyzed by internal sequencing analysis, but very accurate peptides masses can be obtained, which provides additional information useful in both amino acid assignment and database searching.
  • PVDF-bound proteins are suitable for both N-terminal and internal Edman sequencing analysis. PVDF-bound proteins are digested with the proper enzyme (trypsin, endoproteinase Lys-C, endoproteinase GIu-C, clostripain, endoproteinase Asp-N, thermolysin) and a non-ionic detergent such as hydrogenated Triton X-10O. In PVDF bound proteins, the detergents used for releasing digested peptides from the membrane can interfere with MALDI-TOF MS analysis. Before the enzyme is added, Cys is reduced with DTT and alkylated with iodoacetamide to generate carboxyamidomethyl Cys, which can be identified during N-terminal sequence analysis.
  • the proper enzyme trypsin, endoproteinase Lys-C, endoproteinase GIu-C, clostripain, endoproteinase Asp-N, thermolysin
  • a non-ionic detergent
  • the sample is hydrolyzed using phenol catalyzed strong hydrochloric acid (HCl) acidic conditions in the gaseous phase.
  • HCl hydrochloric acid
  • the liberated amino acids are derivatised with a fluorophore compound that imparts a specific reversed phase characteristic on the combined molecule.
  • the derivatized amino acids are separated using reversed phase high performance liquid chromatography (RP-HPLC) and detected with a fluorescence detector.
  • RP-HPLC reversed phase high performance liquid chromatography
  • Peptide mass fingerprinting is another method by which the identity of a protein or chimeric molecule thereof may be determined.
  • the procedure involves an initial separation of the sample by electophoretic means (either 1 or 2 dimensional), excision of the spot/band from the gel and digestion with a specific endoprotease (typically porcine trypsin). Peptides are eluted from the gel fragment and analysed by mass spectrometry to determine the peptide masses present. The resultant peptide masses are then compared to a database of theoretical mass fragments for all reported proteins (or in the case of constructs for the theoretical peptide masses of the designed sequence). The technique relies on the fact that the "fingerprint" of a protein (i.e.
  • HPLC is classified into different modes depending on the size, charge, hydrophobicity, function or specific content of the target biomolecules. Generally, two or more cliromatographic methods are used to purify a protein. It is of paramount importance to consider both the characteristics of the protein and the sample solvent when the chromatographic modes are selected.
  • the secondary structure of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • Electromagnetic energy can be defined as a continuous waveform of radiation, depending on the size and shape of the wave. Different spectroscopic methods use different electromagnetic energy.
  • the wavelength is the extent of a single wave of radiation (the distance between two successive maxima of the waves). When the radiant energy increases, the wavelength becomes shorter.
  • the relationship between frequency and wavenumber is:
  • Wavenumber (cm -1 ) Frequency (s -1 ) / The speed of light (cm/s).
  • the absorption of electromagnetic radiation by molecules includes vibrational and rotational transitions, and electronic transitions.
  • Infrared (IR) and Raman spectroscopy are most commonly used to measure the vibrational energies of molecules in order to determine secondary structure. However, they are different in their approach to determine molecular absorbance.
  • the energy of the scattered radiation is less than the incident radiation for the Stokes line.
  • the energy of the scattered radiation is more than the incident radiation for the anti-Stokes line.
  • the energy increase or decrease from the excitation is related to the vibrational energy spacing in the ground electronic state of the molecule. Therefore, the wavenumber of the Stokes and anti-Stokes lines are a direct measure of the vibrational energies of the molecule.
  • the Stokes lines are at smaller wavenumbers (or higher wavelengths) than the exciting light.
  • a high power excitation source such as a laser, should be used to enhance the efficiency of Raman scattering.
  • the excitation source should be monochromatic because we are interested in the energy (wavenumber) difference between the excitation and the Stokes lines.
  • the dipole moment of the molecule must change. Therefore, the symmetric stretch in carbon dioxide is not IR active because there is no change in the dipole moment. The asymmetric stretch is IR active due to a change in dipole moment.
  • the polarizability of the molecule must change with the vibrational motion.
  • the symmetric stretch in carbon dioxide is Raman active because the polarizability of the molecule change.
  • Raman spectroscopy complements IR spectroscopy (Herzberg et al. Infrared and Raman Spectra of Polyatomic Molecules, Van Nostrand Reinhold, New York, NY, 1945).
  • IR is not able to detect a homonuclear diatomic molecule due to the lack of dipole moments, but Raman spectroscopy can detect it because the molecular polarizability is changed by stretching and contraction of the bond, further, the interactions between electrons and nuclei are changed.
  • IR spectra can provide qualitative and quantitative information of the secondary structures of proteins, such as ⁇ helix, ⁇ sheet, ⁇ turn and disordered structure.
  • the most informative IR bands for protein analysis are amide I (1620-1700 cm -1 ), amide II (1520-1580 cm '1 ) and amide III (1220-1350 cm '1 ).
  • Amide II is governed by in-plane N-H bending (40-60%), C-N (18-40%) and C-C (10%) stretching vibrations.
  • Amide III bands are not very useful (Krimm and Bandekar, Adv Protein Chem 38: 181-364, 1986). Most of the ⁇ - sheet structures of FTIR amide I band usually are located at about 1629 cm -1 with a minimum of 1615 cm -1 and a maximum of 1637 cm -1 ; the minor component may show peaks around 1696 cm -1 (lowest value 1685 cm -1 ), ⁇ -helix is mainly found at 1652 cm -1 . An absorption near 1680 cm -1 is now assigned to ⁇ turns.
  • Raman scattering is different from that of infrared absorption.
  • Raman spectroscopy measures the wavelength and intensity of inelastically scattered light from molecules.
  • the Raman scattered light occurs at wavelengths that are shifted from the incident light by the energies of molecular vibrations.
  • Circular dichroism can be used to detect any asymmetrical structures, such as proteins.
  • Optically active chromophores absorb different amount of right and left polarized light, this absorbance difference results in either a positive or negative absorption spectrum (Usually, the right polarized spectrum is subtracted from the left polarized spectrum).
  • the far UV or amide region (190-250nm) is mainly contributed from peptide bonds, providing information on the environment of the carbonyl group of the amide bond and consequently the secondary structure of the protein, ⁇ -helix usually displays two negative peaks at 208, 222 nm (Holzwarth et al.
  • Intense dichroism is commonly associated with the side-chain structures being held tightly in a highly folded, three-dimensional structure. Denaturation of the protein mostly releases the steric hindrance, a weaker CD spectrum is obtained along with an increasing degree of denaturation. For example, the side chain CD spectrum of hGH is quite sensitive to the partial denaturation by adding denaturants. Some reversible chemical alterations of the molecules, such as reduction of the disulfide bonds, or alkaline titrations will change the side-chain CD spectrum.
  • these spectral difference can be caused by entirely the removal of a chromophores, or by affecting changes in the particular chromophore's CD response, but not by the gross denaturation or conformational changes (Aloj et al. J Biol Chem 247:1146-1151, 1971).
  • UV absorption spectroscopy is one of the most significant methods to determine protein properties. It can provide information about protein concentrations and the immediate environments of chromophoric groups. Proteins functional groups, such as amino, alcoholic (or phenolic) hydroxyl, carbonyl, carboxyl, or thiol can be transformed into strong chromophores. Visible and near UV spectroscopy are used to monitor two types of chromophores: metalloproteins (more than 400 nm) and proteins that contains Phe, Trp, Tyr residues (260-280nm). The change in UV or fluorescence signal can be negative or positive, depending on the protein sequence and solution properties.
  • Proteins functional groups such as amino, alcoholic (or phenolic) hydroxyl, carbonyl, carboxyl, or thiol can be transformed into strong chromophores. Visible and near UV spectroscopy are used to monitor two types of chromophores: metalloproteins (more than 400 nm) and proteins that contains Phe, Trp
  • a signal ratio can be used. For example, In the study of rFXIII unfolding, a ratio of fluorescence intensity at 350nm to that at 330nm was used (Kurochkin et al. J MoI Biol 248:414-430, 1995). Conformational changes may be studied by means of excitation- energy transfer between a fluorescent donor and an absorbing acceptor, because the efficiency of transfer depends on the distance between the two chromophores (Honroe et al. Biochem J 258:199-204, 1989).
  • the tertiary and quaternary structures of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • NMR and X-ray crystallography are the most often used techniques to study the 3D structure of proteins.
  • Other less detailed methods to probe protein tertiary structure include CD in near UV region, second-derivative of UV spectroscopy (Ackland et al. J Chromatogr 540:187-198, 1991) and fluorescence.
  • NMR is one of the main experimental methods for molecular structure and intermolecular interactions in structural biology. In addition to studying protein structures, NMR can also be utilised to study the carbohydrate structures of a protein or chimeric molecule of the present invention. NMR spectroscopy is routinely used by chemists to study chemical structure using simple one-dimensional techniques. The structure of more complicated molecules can also be determined by two-dimensional techniques. Time domain NMR are used to probe molecular dynamics in solutions. Solid state NMR is used to determine the molecular structure of solids. NMR can be used to study structural and dynamic properties of proteins, nucleic acids, a variety of low molecular weight compounds of biological, pharmacological and medical interests.
  • nuclei possess the correct property in order to be read by NMR, i.e., not all nuclei posses spin, which is required for NMR.
  • the spin causes the nucleus to produce an NMR signal, functioning as a small magnetic field.
  • the crystal structure of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • X-ray crystallography is an experimental technique that applies the fact that X-rays are diffracted by crystals.
  • X-rays have the appropriate wavelength (in the Angstrom range, ⁇ 10-8 cm) to be scattered by the electron cloud of an atom of comparable size.
  • the electron density can be reconstructed based on the diffraction pattern obtained from X-ray scattering off the periodic assembly of molecules or atoms in the crystal. Additional phase information either from the diffraction data or from supplementing diffraction experiments should be obtained to complete the reconstruction.
  • a model is then progressively built into the experimental electron density, refined against the data and the result is a very accurate molecular structure.
  • X ray diffraction has been developed to study the structure of all states of matter with any beam, e.g., ions, electrons, neutrons, and protons, with a wavelength similar to the distance between the atomic or molecular structures of interest.
  • Light scattering spectroscopy is based on the simple principle that larger particles scatter light more than the smaller particles.
  • a slope base line in the 310-400nm region originates from light scattering when large particles, such as aggregates, present in the solution (Schmid et al. Protein structure, a practical approach, Creighton Ed., IRI Press, Oxford, England, 1989)
  • Light scattering spectroscopy can be used to estimate the molecular weight of a protein and is a simple tool to monitor protein quaternary structure or protein aggregation. The degree of protein aggregation can be indicated by simple turbidity measurement. Final product pharmaceutical solutions are subjected to inspection of clarity because most aggregated proteins are present as haze and opalescence.
  • Quasielastic light scattering spectroscopy (QELSS), sometimes called photon correlation spectroscopy (PCS), or dynamic light scattering (DLS), is a noninvasive probe of diffusion in complex fluids for macromolecules (proteins, polysaccharides, synthetic polymers, micelles, colloidal particles and aggregations).
  • a protein or chimeric molecule of the present invention may be more stable for lyophilization (freeze drying). Lyophilization is used to enhance the stability and/or shelf life of the product as it is stored in powder rather than liquid form. The process involves an initial freezing of the sample, then removal of the liquid by evaporation under vacuum. The end result is a dessicated "cake" of protein and excipients (other substances used in the formulation). The consistency of the resulting cake is critical for successful reconstitution.
  • the lyophilization process can result in changes to the protein, especially aggregate formation though crosslinking, but also deamidation and other modifications. These can reduce efficacy by either losses, reduced activity or by inducing immune reactions against aggregates.
  • the protein can be formulated for lyophilization using standard stabilizers (e.g. mannitol, trehalose, Tween 80, human serum albumin and the like). After lyophilization, the amount of protein recovered can be assayed by ELISA, while its activity can be assayed by a suitable bioassay. Aggregates of the protein can be detected by HPLC or Western blot analysis.
  • standard stabilizers e.g. mannitol, trehalose, Tween 80, human serum albumin and the like.
  • the Tg or Te (define Tg or Te) of the formulation should be determined to set the maximum allowable temperature of the product during primary drying. Also, information about the crystallinity or amorphousity of the formulation helps to design the lyophilization cycle in a more rationale manner. Product information on these thermal parameters can be obtained by using differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) or freeze-dry cryostage microscope.
  • DSC differential scanning calorimetry
  • TGA thermogravimetric analysis
  • freeze-dry cryostage microscope freeze-dry cryostage microscope.
  • DSC Differential Scanning Calorimetry
  • DSC is a physical thermo-analytical method to measure, characterize and analyze thermal properties of materials and determine the heat capacities, melting enthalpies and transition points accordingly.
  • DSC scans through a temperature range at a linear rate.
  • Individual heaters within the instrument provide heat to sample and reference pans separately, based on the "power compensated null balance" principle.
  • the absorption or evolution of the energy causes an imbalance in the amount of energy supplied to that of the sample holder.
  • the energy will be taken or diffused from the sample, and the temperature difference will be sensed as an electrical signal to the computer.
  • an automatic adjustment of the heaters makes the temperature of the sample holder identical to the reference holder.
  • the electrical power needed for the compensation is equivalent to the calorimetric effect.
  • the purity of an organic substance can be estimated by DSC based on the shape and temperature of the DSC melting endotherm.
  • the power-compensated DSC provides very high resolution compared to a heat flux DSC under the identical conditions. More well-defined and more accurate partial areas of melting can be generated from power- compensated DSC because the partial areas of melting are not "smeared" over a narrow temperature interval, as for the lesser-resolved heat flux DSC.
  • the power-compensated DSC produces inherently better partial melting areas and therefore better purity analysis.
  • StepScan DSC the power-compensated DSC can provide a direct heat capacity measurement using the traditional and time-proven means without the need for deconvolution or the extraction of sine wave amplitudes.
  • TGA Thermogravimetric Analysis
  • freeze-dry cryostage can reach a wide temperature range rapidly.
  • simulating the lyophilization cycle in a freeze dry cryostage provides the best platform to study thermal parameters of the protein formulations on a miniature scale.
  • Freeze dry microscope can predict the influence of formulations and process factors on freezing and drying. Only a 2-3mL sample is required for a cryostage study, which makes this technique a valuable tool to study scarce, diff ⁇ cult- to-obtain drugs. It is a good tool to study the effect of freezing, rate, drying rate, thawing rate on the lyophilization cycle.
  • Annealing research may be advanced by the studies from freeze-dry cryostage microscope. Because of extensive applications of lyophilization technology, and larger demand to stabilize the extremely expensive drugs (such as proteins and gene therapy drugs), it is expected that an in-process microscopic monitor should be realized in the pharmaceutical industries soon.
  • freeze-thaw resistance of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • Co- or post translational modification such as glycosylation may protect proteins from repeated freeze/thaw cycles.
  • a protein or chimeric molecule of the present invention can be compared to carrier-free E. co/z-produced counterparts.
  • a protein or chimeric molecule thereof are diluted into suitable medium (e.g. cell growth medium, PBS or the like) then frozen by various methods, for instance, snap frozen in liquid nitrogen, slowly frozen by being placed at -70 degrees or rapidly frozen on dry ice.
  • the samples are then thawed either rapidly at room temperature or slowly at 4 degrees. Some samples are then refrozen and the process are repeated for a number of cycles.
  • the amount of protein present can be measured by ELISA, and the activity measured in a suitable bioassay chosen by a skilled artisan.
  • the amount of activity/protein remaining is compared to the starting material to determine the resistance over many the freeze/thaw cycles.
  • a protein or chimeric molecule of the present invention may have altered thermal stability in solution.
  • the thermal stability of the present invention may be detennined in vitro as follows.
  • a protein or chimeric molecule of the present invention can be mixed into buffer e.g. phosphate buffered saline containing carrier protein e.g. human serum albumin and incubated at a particular temperature for a particular time (e.g. 37 degrees for 7 days).
  • the amount of protein or chimeric molecule thereof remaining after this treatment can be determined by ELISA and compared to material stored at -70 degrees.
  • the biological activity of the remaining protein or chimeric molecule thereof is determined by performing a suitable bioassay chosen by a person skilled in the relevant art.
  • the protease resistance of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • solution containing a protein or chimeric molecule of the present invention and solution containing E. coli expressed counterparts can be incubated with a protease of choice (e.g. unpurified serum proteases, purified proteases, recombinant proteases) for different time periods.
  • a protease of choice e.g. unpurified serum proteases, purified proteases, recombinant proteases
  • the amount of protein remaining is measured by an appropriate ELISA (e.g. one in which the epitopes recognized by the capture and detection antibodies are separated by the protease cleavage site), and the activity of the remaining protein or chimeric molecule thereof is determined by a suitable bioassay chosen by a skilled artisan.
  • bioavailability of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • Bioavailability is the degree to which a drug or other substance becomes available to the target tissue after administration. Bioavailability may depend on half life of the drug or its ability to reach the target tissue.
  • compositions comprising a protein or chimeric molecule of the present invention is injected subcutaneously or intramuscularly.
  • the levels of the protein or its chimeric molecule can then be measured in the blood by ELISA or radioactive counts.
  • the blood samples can be assayed for activity of the proteinby a suitable bioassay chosen by a skilled artisan, for instance, stimulation of proliferation of a particular target cell population.
  • a suitable bioassay chosen by a skilled artisan, for instance, stimulation of proliferation of a particular target cell population.
  • the sample will be from plasma or serum, there may be a number of other molecules that could be responsible for the output activity. This can be controlled by using a neutralizing antibody to the protein being tested. Hence, any remaining bioactivity is due to the other serum components.
  • the stability or half-life of a protein or chimeric molecule thereof can be assayed using one or more of the following systems.
  • a protein or chimeric molecule of the present invention may have altered half-life in serum or plasma.
  • the half-life of the present invention may be determined in vitro as follows.
  • Composition containing the protein or chimeric molecule of the present invention can be mixed into human serum/plasma and incubated at a particular temperature for a particular time (e.g. 37 degrees for 4 hours, 12 hours etc).
  • the amount of protein or chimeric molecule thereof remaining after this treatment can be determined by ELISA.
  • the biological activity of the remaining protein or chimeric molecule thereof is determined by performing a suitable bioassay chosen by a person skilled in the relevant art.
  • the serum chosen may be from a variety of human blood groups (e.g. A, B, AB, O etc.)
  • composition containing a protein or chimeric molecule thereof can be injected intravenously, subcutaneously, retro- orbitally, tail vein, intramuscularly or intraperitoneally) into the species of choice for the study, for instance, mouse, rat, pig, primate, human. Blood samples are taken at time points after injection and assayed for the presence of the protein or chimeric molecule thereof (either by ELISA or by TCA-precipitable radioactive counts).
  • a comparison composition consisting of E. coli or CHO-produced protein or chimeric molecule thereof can be run as a control.
  • 200 ⁇ l of EDTA blood is sampled as negative control.
  • 200 ⁇ l EDTA blood can be taken from the animals using the same technique. After the last blood sampling, the animals are sacrificed. The specimen is centrifuged for 15 min at RT within 30 min of collection. The plasma samples are tested in a specific ELISA to determine the concentration of protein or chimeric molecule of the present invention in each sample.
  • a protein or chimeric molecule of the present invention may cross the blood brain barrier.
  • Radiolabeled protein or chimeric molecule of the present invention can be tested for its ability to bind to human brain capillary endothelial cells.
  • An isolated protein or chimeric molecule of the present invention can be custom conjugated with radiolabel to a specific activity using a method known in the art, for instance, with 125 I by the chloramine T method, or with 3 H.
  • a human-specific protein or chimeric molecule of the present invention are tested for binding to human brain capillaries using sections of human brain tissue that are fresh frozen (without fixation), sectioned on a cryostat, placed on glass slides and fixed in acetone. Binding of H-protein or chimeric molecule of the present invention is examined on brain sections using quantitative autoradiography.
  • In vivo assay can be used to measure tissue distribution and blood clearance of human- specific protein or chimeric molecule of the present invention in a primate system.
  • a protein or chimeric molecule of the present invention is used to determine the tissue distribution and blood clearance of 14 C -labeled protein or chimeric molecule of the present invention in 2 male cynomolgus monkeys or other suitable primates, protein or chimeric molecule of the present invention is administered concurrently with a 3 H -labeled control protein to the animals with an intravenous catheter.
  • blood samples are collected to determine the clearance of the proteins from the circulation.
  • the animals are euthanized and selected organs and representative tissues collected for the determination of isotope distribution and clearance by combustion.
  • capillary depletion experiments are performed to samples from different regions of the brain in accordance with Triguero, et al. JofNeurochemistry 54: 1882-1888, 1990. This method removes greater than 90% of the vasculature from the brain homogenate (Triguero et al. cited supra).
  • the time-dependent redistribution of the radiolabeled protein or chimeric molecule of the present invention from the capillary fraction to the parenchyma fraction is consistent with the time dependent migration of a protein or chimeric molecule of the present invention across the blood-brain barrier.
  • a protein or chimeric molecule of the present invention may promote or inhibit angiogenesis.
  • the angiogenic potential of the protein or chimeric molecule of the present invention may be assessed methods known in the art.
  • the extent of angiogenesis may be measured by microvessel sprouting in a model of angiogenesis.
  • rat fat microvessel fragments RFMFs
  • Epididymal fat pads are harvested from euthanized animals, minced and digested in collagenase.
  • RFMFs and single cells are separated from lipids and adipocytes by centrifugation and suspended in 0.1% BSA in PBS.
  • the RFMF suspension is sequentially filtered to remove tissue debris, single cells, and red blood cells from the fragments.
  • RFMFs are suspended in cold, pH-neutralized rat-tail type 1 collagen at 15,000 RFMF/ml and plated into wells (for example, 0.25 ml/well) of 48-well plate for culture. After polymerization of the collagen, an equal volume of DMEM containing 10% FBS is added to each gel. After formation of the gels, vascular extensions characteristic of angiogenic sprouts appear by day 4 of culture. These sprouts are readily distinguished from the parent vessel fragment by the absence of the rough, smooth-muscle associated appearance.
  • the RFMF 3-D cultures can be treated with the protein or chimeric molecule of the present invention and vessel sprout lengths can be measured at day 5 and 6 of culture.
  • the angiogenic potential of the protein or chimeric molecule of the present invention may also be assessed by an in vivo angiogenesis assay described in Guedez et al. Am J Pathol 162:1431-1439, 2003.
  • This assay consists of subcutaneous implantation of semiclosed silicone cylinders (angioreactors) into nude mice. Angioreactors are filled with extracellular matrix premixed with or without the protein or chimeric molecule of the present invention. Vascularization within angioreactors is quantified by the intravenous injection of fluorescein isothiocyanate (FITC)-dextran before their recovery, followed by spectrofluorimetry. Angioreactors examined by immunofluorescence is able to show cells and invading angiogenic vessels at different developmental stages.
  • FITC fluorescein isothiocyanate
  • a protein or chimeric molecule of the present invention may have a distinct immunoreactivity profile determined by immunoassay techniques, which involve the interaction of the molecule with one or more antibodies directed against the molecule.
  • immunoassay techniques include enzyme-linked immunoabsorbant assays (ELISA), dot blots and immunochromatographic assays such as lateral flow tests or strip tests.
  • the level of the protein or chimeric molecule thereof may be measured using an immunoassay procedure, for example, a commerically purchased ELISA kit.
  • the protein or chimeric molecule of the present invention may have a different immunoreactivity profile to non-human cell expressed protein or chimeric molecule thereof due to the specificity of the antibodies provided in an immunoassay kit.
  • the capture and/or detection antibodies of the immunoassay may be antibodies specifically directed against non-human cell expressed human protein or chimeric molecule thereof.
  • non-human cell expressed human protein or chimeric molecule thereof may result in the exposure of antigenic epitopes which are not exposed on the correctly folded human cell expressed human protein or chimeric molecule thereof. Incorrect folding may arise through, for instance, overproduction of heterologous proteins in the cytoplasm of non-human cells, for example, E. coli (Baneyx Current Opinion in Biotechnology, 70:411-421, 1999). Further, non-human cell expressed human protein or chimeric molecule thereof may have a different pattern of post-translational modifications to that of the protein or chimeric molecule of the present invention.
  • the non- human cell expressed human protein or chimeric molecule thereof may exhibit abnormal quantities and/or types of carbohydrate structures, phosphate, sulfate, lipid or other residues. This may result in the exposure of antigenic epitopes which are not exposed on the protein or chimeric molecule of the present invention. Conversely, an altered pattern of post-translational modifications may result in an absence of antigenic epitopes on the protein or chimeric molecule of the present invention which are exposed on the non-human cell expressed human protein or chimeric molecule thereof.
  • the immunoreactivity profile of a human cell expressed human protein or chimeric molecule thereof may provide an indication of the protein's immunogenicity in the human, as described hereinafter.
  • the immunogenicity of protein or chimeric molecule thereof can be assayed using one or more of the following systems. Most biologic products elicit a certain level of antibody response against them. The antibody response can, in some cases, lead to potentially serious side effects and/or loss of efficacy. For instance, some patients treated with recombinant EPO will generate neutralizing antibodies that also cross-react with the patient's own EPO. In this case, they can develop pure red cell aplasia and be resistant to EPO treatment, resulting in a need for constant dialysis.
  • Immunogenicity is the property of being able to evoke an immune response within an organism. Immunogenicity depends partly upon the size of the substance in question and partly upon how unlike host molecules it is.
  • a protein or chimeric molecule thereof may have altered immunogenicity due to its novel physiochemical characteristics. For instance, the glycosylation structure of a protein or chimeric molecule thereof may shield or obscure the epitope(s) recognized by the antibody and therefore preventing or reducing antibody binding to the protein or chimeric molecule thereof.
  • some antibodies may recognize a glycopeptide epitope not present in the non-glycosylated version of the protein.
  • the ability of patient samples to recognize a protein or chimeric molecule thereof with a distinctive physiochemical form can be determined by various immunoassays, as described herein.
  • a properly designed immunoassay involves considerations directing to appropriate detection, quantitation and characterization of antibody responses.
  • a number of recommendations for the design and optimization of immunoassays are outlined in Mire- Sluis et al. J Immunol Methods 289(1 -2):l-l6, 2004, which is incorporated by reference.
  • protein or chimeric molecule thereof on therapeutic implants can be assayed using one or more of the following systems.
  • the present invention extends to the use of a protein or chimeric molecule thereof to manipulate stem cells.
  • a major therapeutic use of stem cells is in regeneration of tissue, cartilage or bone.
  • the cells are likely to be introduced to the body in a biocompatible three-dimensional matrix.
  • the implant will consist of a mixture of cells, the scaffold, growth factors and accessory components such as biodegradable polymers, proteoglycans and the like. Incorporation of a protein or chimeric molecule thereof into these matrices during their construction is proposed to regulate the behavior of the cells.
  • Such implants may be used for the formation of bone, the growth of neurons from progenitor cells, chondrocyte implantation for cartilage replacement and other applications.
  • Human cell-derived proteins may reduce the quantity and/or variety of xenogeneic proteins from stem cell culture conditions and thereby reduce the risks of infection by non-human pathogens.
  • a protein or chimeric molecule of the present invention may interact differently with the matrix used for the formation of the implant, as well as regulating the cells incorporated within the implant. It is anticipated that the combination of a protein or chimeric molecule of the present invention with the implant components will result in one or more of the following pharmacological traits, such as higher proliferation, enhanced differentiation, maintenance in a desired state of differentiation, greater lineage specificity of differentiation, enhanced secretion of matrix components, better 3-dimensional structure formation, enhanced signaling, better structural performance, reduced toxicity, reduced side effects, reduced inflammation, reduced immune cell infiltrate, reduced rejection, longer duration of the implant, longer function of the implant, better stimulation of the cells surrounding the implant, better tissue regeneration, better organ function, or better tissue remodeling.
  • pharmacological traits such as higher proliferation, enhanced differentiation, maintenance in a desired state of differentiation, greater lineage specificity of differentiation, enhanced secretion of matrix components, better 3-dimensional structure formation, enhanced signaling, better structural performance, reduced toxicity, reduced side effects, reduced inflammation, reduced immune cell infiltrate,
  • the differences in gene expression can be analyzed in cells exposed to a protein or chimeric molecule thereof.
  • Microarray technology enables the simultaneous determination of the mRNA expression of almost all genes in an organism's genome.
  • This method uses gene "chips" in which oligonucleotides corresponding to the sequences of different genes are attached to a solid support. Labeled cDNA derived from mRNA isolated from the cell or tissue of interest is incubated with the chips to allow hybridisation between cDNA and the attached complementary sequence. A control is also used, and following hybridisation and washing the signal from both is compared. Specialised software is used to determine which genes are up or down regulated or which have unchanged expression. Many thousands of genes can be analysed on each chip.
  • the Human Genome U133 (HG-U133) Set consisting of two GeneChip (registered trade mark) arrays, contains almost 45,000 probe sets representing more than 39,000 transcripts derived from approximately 33,000 well-substantiated human genes.
  • the GeneChip (registered trade mark) Mouse Genome 430 2.0 contains over 39,000 transcripts on a single array.
  • This type of analysis reveals changes in the global niRNA expression pattern and therefore differences in the expression of genes not known to be controlled by a particular stimulus may be uncovered.
  • This technology is hence suitable to analyze the induced gene expression associated with protein or chimeric molecule of the present invention.
  • the system could also be used to look at differences in gene expression induced by a protein or chimeric molecule of the present invention as compared to commercially available products.
  • binding ability of a protein or chimeric molecule of the present invention to various substances including extracellular matrix, artificial materials, heparin sulfates, carriers or co-factors can be investigated.
  • a surface is coated with extracellular matrix proteins, including but not limited to collagen, vitronectin, fibronectin, laminin, in an appropriate buffer.
  • extracellular matrix proteins including but not limited to collagen, vitronectin, fibronectin, laminin, in an appropriate buffer.
  • the unbound sites can be blocked by methods known in the art, for instance, by incubation with BSA solution.
  • the surface is washed, for instance, with PBS solutions, then a solution containing the protein to be tested, for instance a protein or chimeric molecule of the present invention, is added to the surface. After coating, the surface is washed and incubated with an antibody that recognizes a protein or chimeric molecule thereof.
  • Bound antibody is then detected, for instance, by an enzyme-linked secondary antibody that recognizes the primary antibody.
  • the bound antibodies are visualized by incubating with the appropriate substrate and observing a colour change reaction.
  • Glycosylated proteins may adhere more strongly to the extracellular matrix proteins than unglycosylated proteins.
  • an equivalent amount (specified by ELISA concentration or bioassay activity units) of a protein or chimeric molecule of the present invention, or a counterpart protein or chimeric molecule thereof expressed by non-human cells, are incubated with matrix coated wells, then following washing of the wells the amount bound is determined by ELISA.
  • the amount bound can be indirectly measured by a drop in ELISA reactivity following incubation of the sample with the coated surface.
  • protein or chimeric molecule thereof to bind artificial materials can be assayed using one or more of the following systems.
  • a surface is coated with artificial material, including but not limited to metals, scaffolds, in an appropriate buffer.
  • the surface is washed, for instance, with PBS solutions, then a solution containing the protein to be tested, for instance a protein or chimeric molecule of the present invention, is added to the surface.
  • the surface is washed and incubated with an antibody that recognizes a protein or chimeric molecule thereof.
  • Bound antibody is then detected, for instance, by a enzyme-linked secondary antibody that recognizes the primary antibody.
  • the bound antibodies are visualized by incubating with the appropriate substrate and observing a color change reaction.
  • an equivalent amount (specified by ELISA concentration or bioassay activity units) of a protein or chimeric molecule of the present invention, and a counterpart protein or chimeric molecule thereof expressed by non-human cells, are incubated with wells coated by artificial materials, the wells are then washed and the amount bound is determined by ELISA.
  • the amount bound can be indirectly measured by a drop in ELISA reactivity following incubation of the sample with the coated surface.
  • a scaffold coated with a protein or chimeric molecule of the present invention is used to seed cells on. The cell growth and differentiation is then monitored and compared to uncoated or differentially coated scaffolds.
  • protein or chimeric molecule thereof to bind to heparin sulfates can be assayed using one or more of the following systems.
  • a protein or chimeric molecule of the present invention is expected to interact differentially with heparin sulfates due to their physiochemical form. These differences are expected to be evident in experimental models of cell proliferation, differentiation, migration and the like.
  • the combination of a protein or chimeric molecule thereof with heparin sulfates is expected to have distinctive pharmacological traits for a given treatment. This may be an increase in serum half-life, bioavailability, reduced immune- related clearance, greater efficacy, reduced dosage fewer side effects and related advantages.
  • protein or chimeric molecule thereof to bind to carriers or co-factors can be assayed using one or more of the following systems.
  • Proteins or chimeric molecules thereof will be bound to other molecules when they are present in plasma. These molecules may be termed “carriers” or “co-factors” and will influence such factors as bioavailability or serum half life.
  • carriers or “co-factors”
  • Incubating purified versions of the proteins in plasma and analyzing the resulting solution by size exclusion chromatography can determine the interaction of a protein or chimeric molecule of the present invention with their binding partners. If the protein or chimeric molecule thereof binds a co-factor, the resulting complex will have a larger molecular weight, resulting in an altered elution time.
  • the complex can be compared for biological activity, in vitro or in vivo half-life and bioavailability.
  • bioassays can be performed to test the activity of a protein or chimeric molecule of the present invention, including assays on cell proliferation, cell differentiation, cell apoptosis, cell size, cytokine/cytokine receptor adhesion, cell adhesion, cell spreading, cell motility, migration and invasion, chemotaxis, ligand-receptor binding, receptor activation, signal transduction, and alteration of subgroup ratios.
  • Cells in a particular embodiment, exponentially growing cells, are incubated in a growth medium in the presence of a protein or chimeric molecule of the present invention. This can be performed in flasks or 96 well plates. The cells are grown for a period of time and then the number of cells is determined by either a direct (e.g. cell counting) or an indirect (MTT, MTS, tritiated thymidine) method. The increase or decrease in proliferation is determined by comparison with a medium only control assay. Different concentrations of protein or chimeric molecule thereof can be used in parallel series of experiments to get a dose response profile. This can be used to determine the ED50 and EDlOO (the dose required to generate the half maximal and maximal response effectively).
  • a direct e.g. cell counting
  • MTS tritiated thymidine
  • the effects of protein or chimeric molecule thereof on cell differentiation or maintenance of cells in an undifferentiated state can be assayed using one or more of the following systems.
  • Cells are incubated in a growth medium in the presence of a protein or chimeric molecule of the present invention. After a suitable period of time, the cells are assayed for indicators of differentiation. This may be the expression of particular markers on the cell surface, cytoplasmic markers, an alteration in the cell dimensions, shape or cytoplasmic characteristics.
  • the markers may include proteins, sugar structures (e.g. glycosaminocglycans such as heparin sulfates, chondroitin sulfates etc.) lipids
  • glycosphingolipids or lipid bilayer components can be assayed by a number of techniques including microscopy, western blot, FACS staining or forward/side scatter profiles.
  • Apoptosis is defined as programmed cell death, and is distinct from other methods of cell death such as necrosis. It is characterized by defined changes in the cells, such as activation of signaling pathways (e.g. Fas, TNFR) resulting in the activation of a subset of proteases know as caspases. Initiator caspase activation leads to the activation of the executioner caspases which cleave a variety of cellular proteins resulting in nuclear fragmentation, cleavage of nuclear lamins, blebbing of the cytoplasm and destruction of the cell. Apoptosis can be induced by protein ligands such as FasL, TNFa and lymphotoxin or by signals such as UV light and substances causing DNA damage.
  • Cells are incubated in a growth medium in the presence of protein or chimeric molecule thereof and or other agents as suitable for the assay. For instance, the presence of agents able to block transcription (actinomycin D) or translation (cycloheximide) may be required. Following incubation for an appropriate period, the number of cells is determined by a suitable method. A decrease in cell number may indicate apoptosis. Other indications of apoptosis may be obtained by staining of the cells, for instance, for annexins or observing characteristic laddering patterns of DNA. Further evidence for the confirmation of apoptosis may be achieved by preventing the expression of apoptotic markers by incubating with cell permeable caspases inhibitors (e.g.
  • a protein or chimeric molecule of the present invention may prevent apoptosis by providing a survival signal through cellular survival pathways such as the Bcl2 or Akt pathways. Activation of these pathways can be confirmed by western blotting for an increase in cellular Bcl2 expression, or for an increase in the activated (phosphorylated) form of Akt using a phospho-specific antibody directed against Akt.
  • cells are incubated in the presence or absence of the survival factor (e.g. IL- 3 and certain immune cells).
  • the survival factor e.g. IL- 3 and certain immune cells.
  • a proportion of cells incubated in the absence of the survival factor will die by apoptosis upon extended culture, whereas cells incubated in sufficient quantities of survival factor will survive or proliferate.
  • Activation of the cellular pathways responsible for these effects can be determined by western blotting, immunocytochemistry and FACS analysis.
  • a protein or chimeric molecule of the present invention is tested for in vitro activity to protect rat-, mouse-and human cortical neural cells from cell death under hypoxic conditions and with glucose deprivation.
  • neural cell cultures are prepared from rat embryos.
  • the cells are maintained in modular incubator chambers in a water-jacketed incubator for up to 48 hours at 37° C, in serum-free medium with 30 mM glucose and humidified 95% air/5%CO 2 (normoxia) or in serum-free medium without glucose and humidified 95% N 2 /5% CO 2 (hypoxia and glucose deprivation), in the absence or presence of the protein or chimeric molecule of the present invention.
  • the cell cultures are exposed to hypoxia and glucose deprivation for less than 24 hour and thereafter returned to normoxic conditions for the remainder of 24 hour.
  • the cytotoxicity is analyzed by the fluorescence of Alamar blue, which reports cell viability as a function of metabolic activity.
  • the neural cell cultures are exposed for 24 hours to 1 mM L-glutamate or a-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) under normoxic conditions, in the absence or presence of various concentrations of the protein or chimeric molecule of the present invention.
  • AMPA a-amino-3-hydroxy-5-methylisoxazole-4-propionic acid
  • the cytotoxicity is analyzed by the fluorescence of Alamar blue, which reports cell-viability as a function of metabolic activity.
  • a protein or its chimeric molecule may affect the growth, apoptosis, development, or differentiation of a variety of cells. These changes can be reflected by, among other measurable parameters, changes in the cell size and changes in cytoplasmic complexity, which are due to intracellular organelle development. For instance, keratinocytes induced to differentiate by suspension culture exhibit downregulation of surface markers such as ⁇ l integrins, an increase in cell size and cytoplasmic complexity.
  • the effects of a protein or chimeric molecule thereof on cell size, or cytoplasmic complexity can be assayed using one or more of the following systems.
  • FACS measures the amount of light scattered off by a cell when a beam of laser is incident on it.
  • An argon laser providing light with a wavelength of 488nm is frequently used.
  • cells treated with a protein or chimeric molecule of the present invention are diluted in sheath fluid and injected into the flow cytometer (FACSVantage SE, Becton Dickinson). Untreated cells act as a control. The cells pass through a beam of light and the amount of forward scattering of the light corresponds to the size of the cells.
  • Changes in intracellular organelle growth and development can also be measured by FACS.
  • the intracellular organelles of the cell scatter light sideways.
  • change in cytoplasmic complexity can be measured by the amount of side scattering of light by the cells by the above method, and the level of complexity of intracellular organelles and the level of granularity of the cell can be estimated by measuring the level of side scatter of light given off by the cells.
  • the effect of a protein or chimeric molecule thereof on cell size or cytoplasmic complexity can be assessed by using FACS to compare the profiles given off by, for instance, 20,000 treated cells with the signals emitted by identical number of untreated cells. By comparing the signals from the different treated populations of cells, the relative changes in cell size and cytoplasmic complexity can be determined.
  • the effects of a protein or chimeric molecule thereof on cell growth, apoptosis, development, or differentiation can be assayed using one or more of the following systems.
  • Protein-induced apoptosis and changes in cell growth or cycles can be assessed by labeling the DNA of treated cells with dyes such as propidium iodine which has an excitation wavelength in the range of 488 nm and emission at 620 nm.
  • Cells undergoing apoptosis has condensed DNA as well as different size and granularity. These factors give specific forward and size scatter profiles as well as fluorescence signal, and hence the population of cells undergoing apoptosis can be differentiated from normal cells.
  • the amount of DNA in a cell also reflects which state of the cell cycle the cell is in. For instance, a cell in G 2 stage will have twice the amount of DNA as a cell in G 0 state.
  • the protein or its chimeric molecule of the present invention may also alter the expression of various proteins.
  • the effects of the protein or chimeric molecule thereof on protein expression by cells can be assayed using one or more of the following systems.
  • the cells can be fixed and permeabilised, then incubated with fluorescence conjugated antibody targeting the epitope of the protein of interest.
  • fluorescence conjugated antibody targeting the epitope of the protein of interest.
  • a large variety of fluorescent labels can be used with an Argon laser system. Fluorescent molecules such as FITC, Alexa Fluor 488, Cyanine 2, Cyanine 3 are commonly used for this experiment.
  • This method can also be used to estimate the changes in expression of surface markers and proteins by labeling non-permeabilised cells where only the epitope exposed on the cell surface can be labeled with antibodies.
  • the effect of a protein or chimeric molecule thereof can be assessed by using FACS to compare the fluorescence signals given off by, for instance, 20,000 treated cells with the signals emitted by identical number of untreated cells.
  • a protein or chimeric molecule of the present may be more or less adhesive to substrates compared to those of a previously known physiochemical form.
  • the interaction may be with protein receptors for sugar structures (e.g. selectins, such as L-selectin and P- selectin), with extracellular matrix components such as fibronectin, collagens, vitronectins, and lamim ' ns, or with non-protein components such as sugar molecules (heparin sulfates, other glycosaminoglycans).
  • selectins such as L-selectin and P- selectin
  • extracellular matrix components such as fibronectin, collagens, vitronectins, and lamim ' ns
  • non-protein components such as sugar molecules (heparin sulfates, other glycosaminoglycans).
  • a protein or chimeric molecule thereof may also interact differently with non-biological origin materials such as tissue culture plastics, medical device components (e.g. stents or other implants) or dental materials. In the case of medical devices this may alter the engraftment rates, the interaction of the implant with particular classes of cell type or the type of linkage formed with the body.
  • any suitable assays for protein adhesion can be employed.
  • a solution containing a protein or chimeric molecule of the present invention is incubated with a binding partner, in a particular embodiment, on an immobilised surface.
  • the amount of the protein or the chimeric molecule present in the solution is assayed by ELISA and the difference between the amount remaining and the starting material is what has bound to the binding partner.
  • the interaction between the protein or the chimeric molecule and an extracellular matrix protein could be determined by first coating wells of a 96 well plate with the ECM protein (e.g. fibronectin). Nonspecific binding is then blocked by incubation with a BSA solution.
  • ECM protein e.g. fibronectin
  • a known concentration of a protein or its chimeric molecule solution is added for a defined period.
  • the solution is then removed and assayed for the amount of protein or its chimeric molecule remaining in solution.
  • the amount bound to the ECM protein can be determined by incubating the wells with an antibody to a protein or its chimeric molecule, then detecting with an appropriate system (either a labeled secondary antibody or by biotin- avidin enzyme complexes such as those used for ELISA).
  • Methods for determining the amount bound to other surfaces may involve hydrolyzing a protein or its chimeric molecule from the inert implant surface, then measuring the amino acids present in the solution.
  • Integrin molecules consist of alpha and beta subunits, and the particular combinations of alpha and beta subunit give rise to the binding specificity to a particular ligand (e.g. a2bl integrin binds collagen, a5bl binds fibronectin etc).
  • the integrins subunits have large extracellular domains responsible for binding ligand, and shorter cytoplasmic domains responsible for interaction with the cytoskeleton. In the presence of ligand, the cytoplasmic domains are responsible for the induction of signal transduction events ("outside in signaling").
  • the affinity of integrins for their ligands can be modulated by extracellular signaling events that in turn lead to changes in the cytoplasmic tails of the integrins ("inside out signaling").
  • Incubation with a protein or chimeric molecule of the present invention can potentially alter cell adhesion in a number of ways. First, it can alter qualitatively the expression of particular integrin subsets, leading to changes in binding ability. Secondly, the amount of a particular integrin expressed may alter, leading to altered cell binding to its target matrix. Thirdly, the affinity of a particular integrin may be altered without changing its surface expression (inside-out signaling). All these changes may alter the binding of cells to either a spectrum of ligands, or alter the binding to a particular ligand.
  • a protein or chimeric molecule of the present invention can be tested in CeIl-ECM adhesion assays which are generally performed in 96 well plate. Wells are coated with matrix, then unbound sites within the wells are blocked with BSA. A defined number of cells are incubated with the coated wells, then unbound cells are washed away and the bound cells incubated in the presence or absence of the protein or the chimeric molecule thereof. The number of cells is determined by an indirect method such as MTTYMTS. Alternatively, the cells are labeled with a radioactive label (e.g. 51 Cr) and a known amount of radioactivity (i.e. cells) is added to each well. The amount of bound radioactivity is determined and calculated as a percentage of the amount loaded.
  • a radioactive label e.g. 51 Cr
  • a known amount of radioactivity i.e. cells
  • Cells also adhere to other cells, for instance, adhesion of one population of cells to a monolayer of another type of cells. To assay for this, the suspension cells added to the monolayer cells would be labeled with radioactivity. The cells are then incubated in the presence or absence of a protein or chimeric molecule thereof. The unbound cells would be washed away and the remaining mixed population of cells can be lysed and assayed for the amount of radioactivity present.
  • a protein or chimeric molecule of the present invention may have altered effects on cell spreading. Initiation of cell spreading is a key step in cell motility and invasive behavior. Cells spreading can be initiated in vitro in a number of ways. Plating a suspension of cells onto ECM components will result in attachment and ligand binding by integrin receptors. This initiates signal transduction events resulting in the activation of a family of the Cdc42, Rac and Rho small GTPases. Activation of these proteins results in actin polymerization and an extension of a lamellipodium, resulting in gradual flattening of the cells and contact of more integrins with their receptors.
  • focal adhesions large structures containing integrins and signaling proteins.
  • Cell spreading can also be initiated by stimulation of adherent cells with growth factors, again resulting in activation of the Cdc42/Rac/Rho proteins and lamellipodium formation.
  • Cell spreading can be quantitated by examining a large number of cells at different time points following stimulation with a protein or chimeric molecule thereof.
  • the area of each cell can be determined using image analysis programs and the percentage of cells spread as well as the degree of cell spreading can be compared with time. More rapid spreading may be initiated by a higher activation of the Cdc42/Rac/Rho pathways, alternatively, temporal, qualitative and quantitative differences in their activation may be observed with a protein or chimeric molecule of the present invention. This in turn may reflect differences in the signaling events induced by the protein or chimeric molecule of the present invention.
  • Cells adherent to a tissue culture dish do not remain statically anchored to one spot, but rather constantly extend and retract portions of their cell body.
  • the cells can be observed to move around the dish, either as isolated single cells or as a cell colony. This motion may be either "random walk" (i.e. not directed in a particular direction), or directional. Both types of motion can be increased by the addition of growth factors.
  • Time-lapse photography can be used to quantitate the overall distance covered by the cells in a given time period, as well as the overall directionality.
  • directional migration cells will move towards a source of chemoattractant by sensing the chemical gradient and orienting their migration machinery towards it.
  • the chemoattractant is a growth factor.
  • Directional migration can be quantitated by providing a source of chemoattractant (e.g. via a thin pipette) then imaging the cells migrating towards it with time-lapse photography.
  • An alternative system for determining directed migration is the Boyden chamber assay.
  • cells are placed in an upper chamber that is connected to a lower chamber via small holes in the partitioning membrane. Growth medium is put in both chambers, but chemoattractant is added only to the lower chamber, resulting in a diffusion gradient between the two chambers. The cells are attracted to the growth factor source and migrate through the holes in the separation membrane and on to the lower side of the membrane. After a number of hours, the membrane is removed and the number of cells that has migrated onto the bottom of the membrane is determined. The process of cellular invasion utilises many of the same components as migration. Cell invasion can be modeled using layers of extracellular matrix through which the cells invade.
  • Matrigel is a mixture of basement membrane components (ECM components, growth factors etc.) that is liquid at 4 degrees but rapidly sets at 37 degrees to form a gel. This can be used to coat the upper surface of a Boyden chamber, and the chemoattractant added to the lower layer. For cells to pass onto the lower surface of the membrane, they must degrade the matrigel using enzymes such as collagenases and matrix metalloproteinases (MMPs) as well as migrating directionally towards the chemoattractant. This assay mimics the various processes required for cellular invasion.
  • ECM components basement membrane components
  • growth factors etc. This assay mimics the various processes required for cellular invasion.
  • the migration of cells toward the chemoattractant can be measured in vitro in a Boyden chamber.
  • a protein or chimeric molecule of the present in invention is placed in the lower chamber and an appropriate target cell population is placed in the upper chamber.
  • migration through a layer of cells may be measured.
  • Coating the upper surface of the well of the Boyden chamber with a confluent sheet of cells, for instance, epithelial, endothelial or fibroblastic cells will prevent direct migration of immune cells through the holes in the well. Instead, the cells will need to adhere to the monolayer and migrate through it towards the protein to be tested.
  • a neutralising antibody can be incubated with the protein in the lower chamber.
  • the substance is included in the lower chamber of the Boyden chamber along with a solution containing known chemotactic ability (this may be a specific chemokine, conditioned medium from a cell source or cells secreting a range of chemokines).
  • a susceptible target cell population is then added to the upper chamber and the assay performed as described above.
  • a protein or chimeric molecule of the present invention may have different ligand-receptor binding abilities.
  • Ligand-receptor binding can be measured by various parameters, for instance, the dissociation constant (Kd), dissociation rate constant (off rate) (k-), association rate constant (on rate) (k + ). Differences in ligand-receptor binding may correlate with different timing and activation of signaling, leading to different biological outcomes.
  • Ligand-receptor binding can be measured and analysed by either Scatchard plot or by other means such as Biacore.
  • a protein or its chimeric molecule labeled with, for instance, radioactively labeled (eg, 125 I), is incubated in the presence of differing amounts of cold competitor of a protein or its chimeric molecule, with cells, or extracts thereof, expressing the corresponding ligand or receptor.
  • the amount of specifically bound labeled protein or its chimeric molecule is determined and the binding parameters calculated.
  • the corresponding recombinant ligand or receptor of the protein or its chimeric molecule is coupled to the detection unit.
  • Solutions containing a protein or chimeric molecule thereof of choice are then passed over the detection cell and binding is determined by a change in the properties of the detection unit.
  • On rates can be determined by passing solutions containing the protein or the chimeric molecule over the detection cell until a fixed reading is recorded (when the available sites are all occupied).
  • a solution not containing the protein or the chimeric molecule is then passed over the cell and the protein dissociates from the corresponding ligand or receptor, giving the off rate.
  • the effects of a protein or chimeric molecule thereof on receptor activation can be assayed using one or more of the following systems.
  • Interaction with a protein or a chimeric molecule thereof and its corresponding ligand or receptor may be paralleled by differences in the signaling events induced from the cell's endogenous protein.
  • the timing of interaction may be characteristic of a protein or chimeric molecule thereof as definitely on/off rates or dissociation constants.
  • Activated receptors are often internalized by the cells.
  • the receptor/ligand complex can then be dissociated (e.g., be lowering the pH within cellular vesicles, resulting in detachment of the ligand) and the receptor recycled to the cell surface.
  • the complex may be targeted for destruction.
  • the receptors are effectively down- regulated and unable to generate more signal, whereas when they are recycled they are able to repeat the signaling process. Differential receptor binding or activation may result in the receptor being switched from a destruction to a recycling pathway, resulting in a stronger biological response.
  • Binding of ligands or receptors to the protein or its chimeric molecule thereof may initiate signaling, which may include reverse signaling, through a variety of cytoplasmic proteins. Reverse signaling occurs when a membrane-bound form of a ligand transduces a signal following binding by a soluble or membrane bound version of its receptor. Reverse signaling can also occur after binding of the membrane bound ligand by an antibody. These signaling events (including reverse signaling events) lead to changes in gene and protein expression.
  • a protein or chimeric molecule of the present invention can induce or inhibit different signal transductions in various pathways or other signal transduction events, such as the activation of JAK/STAT pathway, Ras-erk pathway, AKT pathway, the activation of PKC, PKA, Src, Fas, TNFR, NFkB, p38MAPK, c-Fos, recruitment of proteins to receptors, receptor phosphorylation, receptor internalization, receptor cross-talk or secretion.
  • the ligands or receptors recruited to the protein or chimeric molecule thereof may be unique to the protein or chimeric molecule of the present invention, due to different conformations of the ligand or receptors being induced.
  • One way of assaying for these differences is to immunoprecipitate the ligand or receptor using an antibody crosslinked to sepahrose beads. Following immunoprecipitation and washing, the proteins are loaded on a 2D gel and the comparative spot patterns are analysed. Different spots can be cut out and identified by mass spectrometry.
  • Cells may have a variety of responses to the protein or chimeric molecule of the present invention.
  • Typical proteins found on the cells surface includes receptors, binding proteins, regulatory proteins and signaling molecules. Changes in expression and degradation rate of the proteins also changes the level of the proteins on the cell surface. Some proteins are also stored in intracellular reservoirs where specific signals can induce trafficking of proteins between this storage and the cellular membrane.
  • Cells are incubated for an appropriate amount of time in medium containing a protein or chimeric molecule of the present invention and their responses can be compared with cells exposed to the same medium without the protein or chimeric molecule of the present invention.
  • the proteins on the cell membrane can be solubilised and separated from the cells by centrifugation.
  • the level of expression of a specific protein can be measured by Western blotting.
  • Cells can also be labeled with fluorescence conjugated antibodies, and visualized under confocal microscopy system or counted by fluorescence activated cell sorting (FACS). This will detect any changes in expression and distribution of proteins on the cells.
  • FACS fluorescence activated cell sorting
  • Cells induced to differentiate in vitro or in vivo by the addition of the protein or chimeric molecule of the present invention will express differentiation markers that distinguish them from the untreated cells. Some cells, for instance, progenitor or stem cells, can differentiate into many subpopulations, distinguishable by their surface markers.
  • a protein or chimeric molecule of the present invention may stimulate the progenitor cells to differentiate into subgroups in a particular ratio.
  • the protein of the present invention and its chimeric molecule may have effects upon cell repulsion.
  • Disrupting the interactions between subunits and other components of a protein leads to a way to inhibit the biological effects of the protein or its chimeric molecule.
  • Compounds inhibiting such biological effects are identified by a number of ways.
  • High throughput screening programs use a library of small chemical entities (chemicals or peptides) to generate lead compounds for clinical development.
  • a number of assays can be used to screen a library compounds for their ability to affect a biologically relevant endpoint. Each potential compound in a library is tested with a particular assay in a single well, and the ability of the compound to affect the assay determined.
  • cells are plated into a microtitre plate (96 plate, 384 plate or the like).
  • the cells will have a readout mechanism for activation of a protein or chimeric molecule thereof. This may involve assaying for cell growth, assaying for stimulation of a particular pathway (e.g., FRET based techniques), assaying for induction of a reporter gene (e.g., CAT, beta-galactosidase, fluorescent proteins), assaying for apoptosis and assaying for differentiation.
  • Cells are then exposed to the protein or chimeric molecule of the present invention in the presence or absence of a particular small molecule.
  • the drug can be added before, after or during the addition of the protein or chimeric molecule thereof.
  • the individual wells are read using an appropriate method (eg, Fluorescence for FRET or induction of fluorescent proteins, cell number by MTT, beta- galactosidase activity etc).
  • Control wells without addition of any drug or cytokine serve as comparisons. Any molecule able to inhibit the receptor/cytokine complex will give a different readout to the control wells. Further experiments will be required to show specificity of the inhibition.
  • the drug could affect the detection method by a non-cytokine, non-receptor mechanism (a false positive).
  • a ligand or receptor of the protein or chimeric molecule thereof is immobilised on a solid surface.
  • a protein or its chimeric molecule and the compound to be tested are then added. This can be performed by adding a protein or its chimeric molecule first, then the compound; the compound first, then a protein or its chimeric molecule; or the compound and the protein or its chimeric molecule can be added together. Bound protein or the chimeric molecule is then detected by an appropriate detection antibody.
  • the detection antibody can be labeled with an enzyme (e.g., alkaline phosphatase or Horse-radish peroxidase for colorimetric detection) or a fluorescent tag for fluorescence detection.
  • a protein or its chimeric molecule can be labeled (e.g., Biotin, radioactive labeling) and be detected with an appropriate technique (e.g., for Biotin labeling, streptavidin linked to a colorimetric detection system, for radiolabeling the complex is solubilised and counted). Inhibition of protein binding is measured by a drop in the reading compared to the control wells.
  • an appropriate technique e.g., for Biotin labeling, streptavidin linked to a colorimetric detection system, for radiolabeling the complex is solubilised and counted. Inhibition of protein binding is measured by a drop in the reading compared to the control wells.
  • Soluble ligands or receptors of the protein or chimeric molecules thereof are bound to beads.
  • This binding reaction can be either an adsorption process or involve chemically linking them to the plate.
  • the beads are incubated with the protein or the chimeric molecules and a candidate compound in an appropriate well. This can be performed as the protein or the chimeric molecules first, then compound; compound first then the protein or the chimeric molecules; or compound and the protein or the chimeric molecules together.
  • a fluorescently labeled detection antibody that recognizes a protein or chimeric molecule thereof is then added. The unbound antibody is removed and the beads are passed through a FACS. The amount of fluorescence detected will decrease if a compound inhibits the interaction of a protein or chimeric molecule thereof with its receptor.
  • a number of different proteins are each linked to beads of a particular diameter.
  • a mixture of ligands/receptors to the above-mentioned proteins are then added to the bead mixture in the presence of one candidate compound.
  • the bound ligands/receptors are then detected using a specific secondary antibodies that is fluorescently labeled.
  • the antibodies can be all labeled with the same detection fluorophore.
  • the ability of the compound to prevent binding of a protein to its ligand/receptor is then determined by running the sample though a FACS machine and gating for each known bead size. The individual binding results are then analysed separately.
  • the major benefit of this method of analysis is that the screening each compound can be tested in parallel with a number of proteins to decrease the time taken for screening proportionally.
  • a protein or chimeric molecule thereof may also be characterised by its crystal structure.
  • the physiochemical form of a protein or its chimeric molecule may provide a unique 3D crystal structure.
  • the crystal structure of the protein-ligand/receptor complex may also be generated using a protein or chimeric molecule of the present invention. Since the present invention provides a protein or a chimeric molecule thereof which is substantially similar to a human naturally occurring form, the complex is likely to be a more reflective representation of the in vivo structure of the naturally occurring protein- ligand/receptor complex. Once a crystal structure has been obtained, interactions between a protein or its chimeric molecule and potential compounds inhibiting such interactions can be identified. Once potential compounds are identified by high throughput screening or from the crystal structure of the protein-ligand/receptor complex, a process of rational drug design can begin.
  • the pharmacophore Once the pharmacophore has been found, its structure is modeled according to its physical properties, e.g. stereochemistry, bonding, size and/or charge, using data from a range of sources, e.g. spectroscopic techniques, x-ray diffraction data and NMR. Computational analysis, similarity mapping (which models the charge and/or volume of a pharmacophore, rather than the bonding between atoms) and other techniques can be used in this modeling process.
  • a range of sources e.g. spectroscopic techniques, x-ray diffraction data and NMR.
  • Computational analysis, similarity mapping which models the charge and/or volume of a pharmacophore, rather than the bonding between atoms
  • other techniques can be used in this modeling process.
  • the three-dimensional structure of the ligand and its binding partner are modeled. This can be especially useful where the ligand and/or binding partner change conformation on binding, allowing the model to take account of this in the design of the mimetic. Modeling can be used to generate inhibitors which interact with the linear sequence or a three-dimensional configuration.
  • a template molecule is then selected onto which chemical groups which mimic the pharmacophore can be grafted.
  • the template molecule and the chemical groups grafted onto it can conveniently be selected so that the mimetic is easy to synthesize, is likely to be pharmacologically acceptable, and does not degrade in vivo, while retaining the biological activity of the lead compound.
  • the mimetic is peptide-based
  • further stability can be achieved by cyclizing the peptide, increasing its rigidity.
  • the mimetic or mimetics found by this approach can then be screened to see whether they have the target property, or to what extent they exhibit it. Further optimization or modification can then be carried out to arrive at one or more final mimetics for in vivo or clinical testing.
  • the goal of rational drug design is to produce structural analogs of biologically active polypeptides of interest or of small molecules with which they interact (e.g. agonists, antagonists, inhibitors or enhancers) in order to fashion drugs which are, for example, more active or stable forms of the polypeptide, or which, e.g. enhance or interfere with the function of a polypeptide in vivo. See, e.g. Hodgson (Bio/Technology 9:19-21, 1991).
  • one first determines the three-dimensional structure of a protein of interest by x-ray crystallography, by computer modeling or most typically, by a combination of approaches. Useful information regarding the structure of a polypeptide may also be gained by modeling based on the structure of homologous proteins.
  • anti-ids anti-idiotypic antibodies
  • the binding site of the anti-ids would be expected to be an analog of the original receptor.
  • the anti-id could then be used to identify and isolate peptides from banks of chemically or biologically produced banks of peptides. Selected peptides would then act as the pharmacore.
  • the protein or chimeric molecule of the present invention is used as an immunogen to generate antibodies.
  • the physiochemical form of a protein or chimeric molecule of the present invention may raise antibodies to the protein or the chimeric molecule; glycopeptides specific to the protein or chimeric molecule of the present invention; or antibodies directed to another co- or post-translationally modified peptide within the protein or chimeric molecule thereof.
  • the protein of the present invention or its chimeric molecule may present epitopes not normally accessible (but possibly present) in vivo. For instance, there may be regions within a receptor domain that are normally in contact with another component of a heteromeric receptor. These epitopes may be used to generate monoclonal antibodies that cross react with the endogenous receptor. Such antibodies may block interaction of one receptor component with another and therefore prevent signal transduction. This may be therapeutically useful in the case of overexpression of a cytokine or receptor. The antibodies may also be therapeutically useful in diseases where the receptor is overexpressed and signals without needing the ligand.
  • the antibodies are also useful to detect the levels of the protein or chimeric molecule thereof during the treatment of the disease (e.g., serum levels for half-life determination).
  • the antibodies are useful as diagnostic for determining the presence of a protein or chimeric molecule of the present invention in a particular sample.
  • an “antibody” or “antibodies” includes reference to all the various forms of antibodies, including but not limited to: full antibodies (e.g. having an intact Fc region), including, for example, monoclonal antibodies; antigen-binding antibody fragments, including, for example, Fv, Fab, Fab' and F(ab') 2 fragments; humanized antibodies; human antibodies (e.g., produced in transgenic animals or through phage display); and immunoglobulin-derived polypeptides produced through genetic engineering techniques. Unless otherwise specified, the terms “antibody” or “antibodies” and as used herein encompasses both full antibodies and antigen-binding fragments thereof.
  • an antibody of the present invention binds substantially only to its target antigen with no appreciable binding to unrelated proteins.
  • an antibody will be designed or selected to bind to two or more related proteins.
  • a related protein includes different splice variants or fragments of the same protein or homologous proteins from different species. Such antibodies are still considered to have specificity for those proteins and are encompassed by the present invention.
  • the term "substantially” means in this context that there is no detectable binding to a non-target antigen above basal, i.e. nonspecific, levels.
  • the antibodies of the present invention may be prepared by well-known procedures. See, for example, Monoclonal Antibodies, Hybridomas: A New Dimension in Biological Analyses, Kennet et al. (eds.), Plenum Press, New York (1980); and Antibodies: A Laboratory Manual, Harlow and Lane (eds.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, (1988).
  • One method for producing an antibody of the present invention comprises immunizing a non-human animal, such as a mouse or a transgenic mouse, with a protein or chimeric molecule of the present invention, or immunogenic parts thereof, such as, for example, a peptide containing the receptor binding domain, whereby antibodies directed against the polypeptide of a protein or its chimeric molecule, or immunogenic parts thereof, are generated in the animal.
  • a protein or chimeric molecule of the present invention or immunogenic parts thereof, such as, for example, a peptide containing the receptor binding domain, whereby antibodies directed against the polypeptide of a protein or its chimeric molecule, or immunogenic parts thereof, are generated in the animal.
  • a protein or chimeric molecule of the present invention or immunogenic parts thereof, such as, for example, a peptide containing the receptor binding domain, whereby antibodies directed against the polypeptide of a protein or its chimeric molecule, or immunogenic parts thereof, are generated in the animal.
  • Immunizations typically involve an initial immunization followed by a series of booster immunizations. Animals may be bled and the serum assayed for antibody titer. Animals may be boosted until the titer plateaus. Conjugates may be made in recombinant cell culture as protein fusions. Also, aggregating agents such as alum are suitably used to enhance the immune response.
  • Both polyclonal and monoclonal antibodies can be produced by this method.
  • the methods for obtaining both types of antibodies are well known in the art.
  • Polyclonal antibodies are less favored but are relatively easily prepared by injection of a suitable animal with an effective amount of a protein or chimeric molecule of the present invention, or immunogenic parts thereof, collecting serum from the animal and isolating specific antibodies to a protein or chimeric molecule thereof by any of the known immunoadsorbent techniques.
  • Antibodies produced by this technique are generally less favoured, because of the potential for heterogeneity of the product.
  • monoclonal antibodies are particularly favored because of the ability to produce them in large quantities and the homogeneity of the product.
  • Monoclonal antibodies may be produced by conventional procedures.
  • the term "monoclonal antibody” as used herein refers to an antibody obtained from a population of substantially homogeneous antibodies, i.e., the individual antibodies comprising the population are identical except for possible naturally occurring mutations that may be present in minor amounts. Monoclonal antibodies are highly specific, being directed against a single antigenic site. Furthermore, in contrast to polyclonal antibody preparations which typically include different antibodies directed against different determinants (epitopes), each monoclonal antibody is directed against a single determinant on the antigen.
  • the modifier "monoclonal” indicates the character of the antibody as being obtained from a substantially homogeneous population of antibodies, and is not to be construed as requiring production of the antibody by any particular method.
  • the monoclonal antibodies to be used in accordance with the present invention may be made by the hybridoma method first described by Kohler et al. Nature 256:495 (1975), or may be made by recombinant DNA methods (see, e.g., U.S. Pat. No. 4,816,567).
  • the "monoclonal antibodies” may also be isolated from phage antibody libraries using for example, the techniques described in Clackson et al. Nature 552:624-628, 1991 and Marks et al. JMoI Biol 222:581-597, 1991.
  • the present invention contemplates a method for producing a hybridoma cell line which comprises immunizing a non-human animal, such as a mouse or a transgenic mouse, with a protein or chimeric molecule of the present invention; harvesting spleen cells from the immunized animal; fusing the harvested spleen cells to a myeloma cell line to generate hybridoma cells; and identifying a hybridoma cell line that produces a monoclonal antibody that binds a protein or chimeric molecule thereof.
  • Such hybridoma cell lines and the monoclonal antibodies produced by them are encompassed by the present invention.
  • Monoclonal antibodies secreted by the hybridoma cell lines are purified by conventional techniques. Hybridomas or the monoclonal antibodies produced by them may be screened further to identify monoclonal antibodies with particularly desirable properties, such as the ability to inhibit cytokine-signaling through its receptor.
  • a protein or chimeric molecule thereof or immunogenic part thereof that may be used to immunize animals in the initial stages of the production of the antibodies of the present invention should be from a human-expressed source.
  • Antigen-binding fragments of antibodies of the present invention may be produced by conventional techniques. Examples of such fragments include, but are not limited to, Fab, Fab', F(ab') 2 and Fv fragments, including single chain Fv fragments (termed sFv or scFv). Antibody fragments and derivatives produced by genetic engineering techniques, such as disulfide stabilized Fv fragments (dsFv), single chain variable region domain (Abs) molecules, minibodies and diabodies are also contemplated for use in accordance with the present invention.
  • dsFv disulfide stabilized Fv fragments
  • Abs single chain variable region domain
  • Such fragments and derivatives of monoclonal antibodies directed against a protein or chimeric molecule thereof may be prepared and screened for desired properties, by known techniques, including the assays herein described.
  • the assays provide the means to identify fragments and derivatives of the antibodies of the present invention that bind to a protein or chimeric molecule thereof, as well as identify those fragments and derivatives that also retain the activity of inhibiting signaling by a protein or chimeric molecule thereof.
  • Certain of the techniques involve isolating DNA encoding a polypeptide chain (or a portion thereof) of a rnAb of interest, and manipulating the DNA through recombinant DNA technology. The DNA may be fused to another DNA of interest, or altered (e.g.
  • DNA encoding antibody polypeptides may be isolated from B-cells of mice that have been immunized with a protein or chimeric molecule of the present invention.
  • the DNA may be isolated using conventional procedures.
  • Phage display is another example of a known technique whereby derivatives of antibodies may be prepared.
  • polypeptides that are components of an antibody of interest are expressed in any suitable recombinant expression system, and the expressed polypeptides are allowed to assemble to form antibody molecules.
  • Single chain antibodies may be formed by linking heavy and light chain variable region (Fv region) fragments via an amino acid bridge (short peptide linker), resulting in a single polypeptide chain.
  • Fv region heavy and light chain variable region
  • Such single-chain Fvs (scFvs) have been prepared by fusing DNA encoding a peptide linker between DNAs encoding the two variable region polypeptides (VL and VH). The resulting antibody fragments can form dimers or trimers, depending on the length of a flexible linker between the two variable domains (Kortt et al. Protein Engineering 10:423, 1997). Techniques developed for the production of single chain antibodies include those described in U.S. Patent No. 4,946,778; Bird (Science 242:423, 1988), Huston et al. (Proc Natl Acad Sci USA 85:5879, 1988) and Ward et al. (Nature 334:544, 1989).
  • Single chain antibodies derived from antibodies provided herein are encompasse
  • the present invention provides antibody fragments or chimeric, recombinant or synthetic forms of the antibodies that bind to the protein or chimeric molecule of the present invention and inhibit signaling by the protein or its chimeric molecule.
  • IgGl or IgG4 monoclonal antibodies may be derived from an IgM monoclonal antibody, for example, and vice versa.
  • Such techniques allow the preparation of new antibodies that possess the antigen-binding properties of a given antibody (the parent antibody), but also exhibit biological properties associated with an antibody isotype or subclass different from that of the parent antibody.
  • Recombinant DNA techniques may be employed. Cloned DNA encoding particular antibody polypeptides may be employed in such procedures, e.g. DNA encoding the constant region of an antibody of the desired isotype.
  • the monoclonal production process described above may be used in animals, for example mice, to produce monoclonal antibodies.
  • Conventional antibodies derived from such animals, for example murine antibodies are known to be generally unsuitable for administration to humans as they may cause an immune response. Therefore, such antibodies may need to be modified in order to provide antibodies suitable for administration to humans.
  • Processes for preparing chimeric and/or humanized antibodies are well known in the art and are described in further detail below.
  • the monoclonal antibodies herein specifically include "chimeric" antibodies in which the variable domain of the heavy and/or light chain is identical with or homologous to corresponding sequences in antibodies derived from a non-human species (e.g., murine), while the remainder of the chain(s) is identical with or homologous to corresponding sequences in antibodies derived from humans, as well as fragments of such antibodies, so long as they exhibit the desired biological activity (U.S. Pat. No. 4,816,567; and Morrison et al. Proc Natl Acad Sci USA 57:6851-6855, 1984).
  • a non-human species e.g., murine
  • Humanized forms of non-human (e.g., murine) antibodies are chimeric antibodies which contain minimal sequence derived from the non-human immunoglobulin.
  • humanized antibodies are human immunoglobulins (recipient antibody) in which the complementarity determining regions (CDRs) of the recipient are replaced by the corresponding CDRs from a non-human species (donor antibody) such as mouse, rat, rabbit or nonhuman primate having the desired properties, for example specificity, and affinity.
  • donor antibody such as mouse, rat, rabbit or nonhuman primate having the desired properties, for example specificity, and affinity.
  • framework region residues of the human immunoglobulin are replaced by corresponding non-human residues.
  • humanized antibodies may comprise residues which are not found in the recipient antibody or in the donor antibody. These modifications are made to further refine antibody performance.
  • the humanized antibody will comprise substantially all of at least one, and typically two, variable domains, in which all or substantially all of the complementarity determining regions correspond to those of a non-human immunoglobulin and all or substantially all of the framework region residues are those of a human immunoglobulin sequence.
  • the humanized antibody optionally also will comprise at least a portion of an immunoglobulin constant region (Fc), typically that of a human immunoglobulin.
  • Fc immunoglobulin constant region
  • the present invention provides an immunoassay kit with the ability to assay the level of human protein expressed from human cells present in a biological preparation, including a biological preparation comprising the naturally occurring human protein.
  • a biological preparation which can be assayed using the immunoassay kit of the present invention includes but is not limited to laboratory samples, cells, tissues, blood, serum, plasma, urine, stool, saliva and sputum.
  • the immunoassay kit of the present invention comprises a solid phase support matrix, not limited to but including a membrane, dipstick, bead, gel, tube or a multi-well, flat- bottomed, round-bottomed or v-bottomed microplate, for example, a 96-well microplate; a preparation of antibody directed against the human protein of interest (the capture antibody); a preparation of blocking solution (for example, BSA or casein); a preparation of secondary antibody (the detection antibody), also directed against the human protein of interest and conjugated to a suitable detection molecule (for example, alkaline phosphatase); a solution of chromagenic substrate (for example, nitro blue tetrazolium); a solution of additional substrate (for example, 5-bromo-4-chloro-3-indolyl phosphate); a stock solution of substrate buffer (for example, 0.1M Tris-HCL (pH 7.5) and 0.1M NaCl, 50mM MgCl 2 ); a preparation of the
  • a suitable detection molecule may be chosen from the list consisting an enzyme, a dye, a fluorescent molecule, a chemiluminescent, an isotope or such agents as colloidal gold conjugated to molecules including, but not limited to, such molecules as staphylococcal protein A or streptococcal protein G.
  • the capture and detection antibodies are monoclonal antibodies, the production of which comprises immunizing a non-human animal, such as a mouse or a transgenic mouse, with a protein or chimeric molecule of the present invention, followed by standard methods, as hereinbefore described.
  • Monoclonal antibodies may alternatively be produced by recombinant methods, as hereinbefore described and may comprise human or chimeric antibody portions or domains.
  • the capture and detection antibodies are polyclonal antibodies, the production of which comprises immunizing a non-human animal, such as a mouse, rabbit, goat or horse, with a protein or chimeric molecule of the present invention, followed by standard methods, as hereinbefore described.
  • the components of the immunoassay kit are provided in predetermined ratios, with the relative amounts of the various reagents suitably varied to provide for concentrations in solution of the reagents that substantially maximize the sensitivity of the assay.
  • the reagents may be provided as dry powders, usually lyophilized, including excipients, which on dissolution provide for each reagent solution having the appropriate concentration for combining with the biological preparation to be tested.
  • the instructions for use may detail the method for using the immunoassay kit of the present invention.
  • the instructions for use may describe the method for coating the solid phase support matrix with a prepared solution of capture antibody under suitable conditions, for example, overnight at 4°C.
  • the instructions for use may further detail blocking non-specific protein binding sites with the prepared blocking solution; adding and incubating serially diluted sample containing the protein or chimeric protein of the present invention under suitable conditions, for example, 1 hour at 37°C or 2 hours at room temperature, followed by a series of washes using a suitable buffer known in the art, for example, a solution of 0.05% Tween 20 in 0.1M PBS (pH 7.2).
  • the instructions may provide that a preparation of detection antibody is applied followed by incubation under suitable conditions, for example, 1 hour at 37°C or 2 hours at room temperature, followed by a further series of washes.
  • a working solution of detection buffer is prepared from the supplied detection substrate(s) and substrate buffer, then added to each well under a suitable conditions ranging from 5 minutes at room temperature to 1 hour at 37°C.
  • the chromatogenic reaction may be halted with the addition of IN NaOH or 2N H 2 SO 4 .
  • the instructions for use may provide the simultaneous addition of any combination of any or all of the above components to be added in predetermined ratios, with the relative amounts of the various reagents suitably varied to provide for concentrations in solution of the reagents that substantially maximize the formation of a measurable signal from formation of a complex.
  • the level of colored product, or fluorescent or chemiluminescent or radioactive or other signal generated by the bound, conjugated detection reagents can be measured using an ELISA-plate reader or spectrophotometer, at an appropriate optical density (OD), or as emitted light, using a spectrophotometer, fluorometer or flow cytometer, at an appropriate wavelength, or using a radioactivity counter, at an appropriate energy spectrum, or by a densitometer, or visually by comparison to a chart or guide.
  • OD optical density
  • fluorometer or flow cytometer at an appropriate wavelength, or using a radioactivity counter, at an appropriate energy spectrum, or by a densitometer, or visually by comparison to a chart or guide.
  • a serially diluted solution of the standard preparation is assayed in parallel with the above sample.
  • a standard curve or chart is generated and the level of the protein or chimeric molecule thereof present within the sample can be interpolated from the standard curve or chart.
  • the subject invention also provides a human derived protein or chimeric molecule thereof for use as a standard protein in an immunoassay.
  • the present invention further extends to a method for determining the level of human cell-expressed human protein or chimeric molecule thereof in a biological preparation comprising a suitable assay for measuring the human protein or the chimeric molecule wherein the assay comprises (a) combining the biological preparation with one or more antibodies directed against the human protein or chimeric molecule thereof; (b) determining the level of binding of the or each antibody to the human protein or the chimeric molecule in the biological preparation; (c) combining a standard human protein or a chimeric molecule sample with one or more antibodies directed against the human protein or the chimeric molecule; (d) determining the level of binding of the or each antibody to the standard human protein or the chimeric molecule sample; (e) comparing the level of the or each antibody bound to the human protein or the chimeric molecule in the biological preparation to the level of the or each antibody bound to the
  • the standard human protein or chimeric molecule sample is a preparation comprising the protein or chimeric molecule of the present invention.
  • the biological preparation includes but is not limited to laboratory samples, cells, tissues, blood, serum, plasma, urine, stool, saliva and sputum.
  • the biological preparation is bound to one or more capture antibody as described hereinbefore or by methods known in the art.
  • the solid phase support matrix is first coated with a prepared solution of capture antibody under suitable conditions (for example, overnight at 4°C); followed by blocking non-specific protein binding sites with the prepared blocking solution; then adding and incubating serially diluted sample containing a protein or chimeric molecule of the present invention under suitable conditions (for example, 1 hour at 37°C or 2 hours at room temperature), followed by a series of washes using a suitable buffer known in the art (for example, a solution of 0.05% Tween 20 in 0.1M PBS (pH 7.2)).
  • suitable buffer for example, a solution of 0.05% Tween 20 in 0.1M PBS (pH 7.2)
  • the biological preparation is then combined with one or more detection antibodies conjugated to a suitable detection molecule as described herein. For instance, applying a preparation of detection antibody followed by incubation under suitable conditions (for example, 1 hour at 37°C or 2 hours at room temperature), followed by a further series of washes.
  • suitable conditions for example, 1 hour at 37°C or 2 hours at room temperature
  • Determination of the level of binding may be carried out as described hereinbefore or by methods known in the art. For instance, a working solution of detection buffer is prepared from the detection substrate(s) and substrate buffer, then adding to each well under a suitable conditions ranging from 5 minutes at room temperature to 1 hour at 37°C. The chromatogenic reaction may be halted with the addition of IN NaOH or 2N H 2 SO 4 .
  • the present invention contemplates an isolated protein or chimeric molecule as hereinbefore described.
  • a TNF-a of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: - an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9,
  • an observed molecular weight of the molecule after the N-linked oligosaccharides are removed (P 6 ) of about 8 to 30 kDa; an observed molecular weight of the molecule after the N-linked and O-linked oligosaccharides are removed (P 7 ) of about 8 to 25 kDa, and in one embodiment, 10 to 20 kDa; an immunoreactivity profile (T 13 ) that is distinct from that of a human TNF-a expressed in a non-human cell system, and in one embodiment, the protein concentration of the TNF-a of the present invention is underestimated when assayed using an ELISA kit which contains a human TNF-a expressed in a non-human cell system.
  • a LT-a of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
  • P 1 apparent molecular weight of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55,
  • an observed molecular weight of the molecule after the N-linked oligosaccharides are removed (P 6 ) of about 10 to 30 kDa and in one embodiment, 12 to 25 kDa; - an observed molecular weight of the molecule after the N-linked and O-linked oligosaccharides are removed (P 7 ) of about 10 to 25 kDa and in one embodiment, 12 to 23 kDa; an immunoreactivity profile (T 13 ) that is distinct
  • a TNFRI-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 5 to 120 kD such as 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80,
  • an observed molecular weight of the molecule after the N-linked oligosaccharides are removed (P 6 ) of about 35 to 65 kDa and in one embodiment, 36 to 60 kDa; an observed molecular weight of the molecule after the N-linked and O-linked oligosaccharides are removed (P 7 ) of about 35 to 65 kDa and in one embodiment, 36 to 60 kDa; a percentage acidic monosaccharide content (P 8 ) of about 0-50%, such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30,
  • N-linked oligosaccharides P 14
  • P 14 an acidic percentage of N-linked oligosaccharides (P 14 ) of about 0 to 50% such as 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50%, and in one embodiment 0
  • P 21 site of N-glycosylation
  • a TNFRII-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (Ty) comprising: an apparent molecular weight (P 1 ) of about 10 to 150, such as 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38,
  • N-linked oligosaccharides P 13
  • P 13 N-linked oligosaccharides
  • O-linked oligosaccharides P 15
  • P 15 O-linked oligosaccharides
  • TNFRII-Fc one or more O-glycan structures as listed in Table 37(b) in the O-linked fraction (P 20 ); a biological activity that is distinct from that of a human TNFRII-Fc expressed in a non-human cell system, and in one embodiment, the ability of TNFRII-Fc of the present invention to neutralise TNF-a induced cytotoxicity (T 30 ) in L-929 cells is 8- 18 fold more potent than a human TNFRII-Fc expressed in E. co ⁇ i cells.
  • an OX40-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
  • N-linked oligosaccharides P 13
  • P 14 an acidic percentage of N-linked oligosaccharides
  • P 15 a neutral percentage of O-linked oligosaccharides
  • P 16 an acidic percentage of O-linked oligosaccharides (P 16 ) of about 0 to 80%, in one embodiment 10 to 60% and a further embodiment, 20 to 55%
  • a BAFF of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94
  • an observed molecular weight of the molecule after the N-linked oligosaccharides are removed (P 6 ) of about 8 to 22 kDa, and in one embodiment, 10 to 22 kDa;
  • an observed molecular weight of the molecule after the N-linked and O-lmked oligosaccharides are removed (P 7 ) of about 8 to 22 kDa, and in one embodiment, 10 to 22 kDa;
  • a biological activity that is distinct from that of a human BAFF expressed in a non- human cell system, and in one embodiment, the ability of BAFF of the present invention to induce proliferation (T 32 ) in RPMI 8226 cells is 1.1-2.4 fold more potent than a
  • a NGFR-Fc of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (T y ) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
  • an observed molecular weight of the molecule following removal of N-linked oligosaccharides (P 6 ) of between 45 and 100 kDa, and in one embodiment, 48 to 90 kDa; - an observed molecular weight of the molecule after the N-linked and O-linked oligosaccharides are removed (P 7 ) of about 45 to 95 kDa, and in one embodiment, 48 to 85 kDa.
  • a Fas Ligand of the present invention is characterized by a profile of one or more of the following physiochemical parameters (P x ) and pharmacological traits (Ty) comprising: an apparent molecular weight (P 1 ) of about 1 to 250, such as 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 61, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78,
  • N-linked oligosaccharides P 6
  • P 21 N-linked oligosaccharides
  • the protein or chimeric molecule of the present invention contains at least one of the following structures in the N-linked fraction (P 19 ).
  • "u” or "?” represents that the anomeric configuration is either a or b, and/or the linkage position is 2, 3, 4, and/or 6.
  • Glycan structure GlcNAc(b1-2)Man(a1-6)[Man(a1-3)]Man(b1-4)GlcNAc(b1- 4)GlcNAc
  • Glycan structure GlcNAc(b1-4)Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b 1 ⁇ 4)GlcNAc
  • Glycan structure GlcNAc(b1-2)Man(a1-3) [Man(a1-6)]Man(b1-4)GlcNAc(b1-4) [Fuc (a1-6)]GlcNAc
  • Glycan structure GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1- 4)GlcNAc (b1-4)GlcNAc
  • Glycan structure GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-4)] [Man(a1-6)]Man(b1-4) GlcNAc(b1-4)GlcNAc
  • Glycan structure Fuc(a1-6) [GlcNAc(b1-4)] GIcNAc
  • Glycan structure GlcNAc(b1-2)Man(a1-6)Man(b1-4)GlcNAc(b1-4)[Fuc(a1- O)]GIcNAc
  • Glycan structure NeuAc(a2-?)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)Man(b1-4)GlcNAc
  • Glycan structure GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man(b1- 4)GlcNAc (b1-4)[Fuc(a1-6)]GIcNAc
  • Glycan structure GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)] [GlcNAc ⁇ 1 - 4)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-4)] [Man(al -6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)] [GlcNAc(b 1 - 4)]Man(b1-4)GlcNAc(b1-4)[Fuc(al -6)] GIcNAc
  • Glycan structure GlcNAc(b1-2) [GlcNAc(b1-4)]Man(a1-3) [GlcNAc(b1-2)Man(al ⁇ 6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc
  • Glycan structure GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-2)Man(al- 6)][GlcNAc(b1-4)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure GlcNAc(b1-2)[GlcNAc(b1-4)]Man(a1-3)[GlcNAc(b1-2)[GlcNAc (b1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure HSO3(-4)GalNAc(b1-4)GlcNAc(b1-2)Man(a1-3)[HSO3(- 4)GalNAc (b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure NeuAc(a2-?)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-6)]Man (b1-4)GlcNAc
  • Glycan structure Fuc(?1-?)[Gal(?1-?)]GlcNAc(?1-?)Man(a1-?)[Man(a1-?)]Man (b1-4)GlcNAc(b1-4)[Fuc(?1-6)]GlcNAc
  • Glycan structure Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man(a1-6)]Man (b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure NeuAc(a2-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[GlcNAc(b1-2)Man (a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Gal(b1-4)GlcNAc(b1-2)Man(a1-6)[GlcNAc(b1-2)Man(a1-3)]Man (b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc
  • Glycan structure NeuAc(a2-6)GalNAc(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1- 4)GlcNAc (b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure NeuAc(a2-?)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-3)Man( al-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)Man (a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-O)]GIcNAc
  • Glycan structure Fuc(a1-2)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc (b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Fuc(a1-2)Gal(b1-4)GlcNAc(b1-2)Man(a1-6)[Gal(b1-4)GlcNAc (b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Fuc(a1-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-6)[NeuAc(a2-6)Gal( b 1 -4)GlcNAc(b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-2)Man(a1-6)[Gal(b1-
  • Glycan structure Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-2)Man(a1-6)[Gal(b1-4)GlcNAc (b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc
  • Glycan structure Fuc(a1-3) [Gal(b1-4)] GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc (b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(a1-6)]GlcNAc
  • Glycan structure Fuc(a1-2)Gal(b1-4)GlcNAc(b1-2)Man(a1-6)[Gal(b1-4)GlcNAc (b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4) [Fuc(a1-6)] GIcNAc
  • Glycan structure NeuAc(a2-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Fuc(a1-3)[Gal (b1-4)]GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc( al -6)] GIcNAc
  • Glycan structure NeuAc(a2-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-6) [Fuc(a1-3) [Gal (b1-4)]GlcNAc(b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)[Fuc( al-6)]GlcNAc
  • Glycan structure Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-2)Man(a1-3)[Fuc(a1-3)[Gal (b1-4)]GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc( al-6)]GlcNAc
  • Glycan structure NeuAc(a2-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-
  • Glycan structure Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal (b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Fuc(a1-2)[GalNAc(a1-3)]Gal(b1-4)GlcNAc(b1-2)Man(a1-6)[Gal (b1-4)GlcNAc(b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Fuc(a1-2)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-4)GlcNAc (b1-2)Man(a1-6)] [GlcNAc(b1-4)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Fuc(a1-2)Gal(b1-4)GlcNAc(b1-2)Man(a1-6) [Gal(b1-4)GlcNAc (b1-2)Man(a1-3)] [GIcNAc(b1-4)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure NeuAc(a2-6)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal(b1-
  • Glycan structure Fuc(a1-2)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Fuc(a1-2)Gal(b 1
  • Glycan structure Fuc(a1-2)[Gal(a1-3)]Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Gal( bl-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)[Fuc(al -O)]GIcNAc
  • Glycan structure Fuc(a1-2)[Gal(a1-3)]Gal(b1-4)GlcNAc(b1-2)Man(a1-6)[Gal( bl-4)GlcNAc(b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)[Fuc(al -O)]GIcNAc Fucal,
  • Glycan structure Gal(b1-4)GlcNAc(b1-2)[Gal(b1-4)GlcNAc(b1-4)]Man(a1-3)[Gal (b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Gal(b1-4)GlcNAc(b1-3)Gal(b1-4)GlcNAc(b1-2)Man(a1-6)[Gal (b1-4)GlcNAc(b1-2)Man(a1-3)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-3)[Man(a1-6)]Man( al-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure NeuAc(a2-?)Gal(b1-4)GlcNAc(b1-2)Man(a1-3)[Man(a1-3)[Man (a1-6)]Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc
  • Glycan structure NeuAc(a2-?)Gal(b1-4)GlcNAc(b1-4)[Gal(b1-4)GlcNAc(b1-2)]
  • Glycan structure NeuAc(a2-?)Gal(b1-4)GlcNAc(b1-2)[Gal(b1-4)GlcNAc(b1-4)] Man(a1-3)[Gal(b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc (b1-4)GlcNAc
  • Glycan structure NeuAc(a2-6)Gal(b1-4)GlcNAc(b1-2)[Gal(b1-4)GlcNAc(b1-4)]
  • Glycan structure NeuAc(a2-3)Gal(b1-4)GlcNAc(b1-2)[NeuAc(a2-3)Gal(b1-
  • Glycan structure Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-4)[Gal(b1-4)GlcNAc(b1-2)]
  • Glycan structure Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-4)[Gal(b1-4)GlcNAc(b1-2)]
  • Glycan structure Gal(b1-4)GlcNAc(b1-2)[Gal(b1-4)GlcNAc(b1-4)]Man(a1-3)[Gal (b1-4)GlcNAc(b1-2)Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc +"+ Fuc(a1-2)"
  • Glycan structure NeuAc(a2-3)Gal(b1-4)GlcNAc(b1-4)[Gal(b1-4)GlcNAc(b1-2)]
  • Glycan structure NeuAc(a2-6)Gal(b1-4)GlcNAc(b1-2)[Fuc(a1-3)[Gal(b1-
  • Glycan structure NeuAc(a2-3)Gal(b1-4)GlcNAc(b1-4)[NeuAc(a2-6)Gal(b1-
  • Glycan structure NeuAc(a2-3)Gal(b1-4)[Fuc(a1-3)]GlcNAc(b1-4)[NeuAc(a2-
  • Glycan structure Fuc(a1-3)[Gal(b1-4)]GlcNAc(b1-4)[Gal(b1-4)GlcNAc(b1-2)]

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Abstract

La présente invention se rapporte d'une manière générale aux domaines des protéines, des diagnostics, de la thérapie et de la nutrition. Plus précisément, la présente invention propose une molécule de protéine isolée qui appartient ou qui est apparentée à la superfamille des facteurs de nécrose des tumeurs (Tumor Necrosis Factor ; TNF) telle que TNF-a, Lymphotoxine-a (LT-a), TNFRI, TNFRII, OX40, BAFF, NGFR, Fas Ligand, de même que des molécules chimériques de celle-ci comprenant au moins une partie de la molécule de protéine, telles que TNF-a-Fc, LT-a-Fc, TNFRI-Fc, TNFRII-Fc, OX40-Fc, BAFF-Fc, NGFR-Fc, Fas Ligand-Fc. La molécule de protéine ou sa molécule chimérique présente un profil de paramètres biochimiques mesurables qui est indicatif d'une ou de plusieurs caractéristiques pharmacologiques, qui est associé à ces caractéristiques pharmacologiques ou qui en forme la base. La présente invention envisage en outre l'utilisation de la protéine isolée ou de sa molécule chimérique dans un éventail d'applications diagnostiques, prophylactiques, thérapeutiques, nutritionnelles et/ou de recherche.
PCT/AU2006/000102 2005-01-28 2006-01-27 Molecules et leurs molecules chimeriques WO2006079176A1 (fr)

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US11/814,566 US20090232808A1 (en) 2005-01-28 2006-01-27 Molecules and chimeric molecules thereof
JP2007552463A JP2008528006A (ja) 2005-01-28 2006-01-27 分子およびそのキメラ分子
AU2006208439A AU2006208439A1 (en) 2005-01-28 2006-01-27 Molecules and chimeric molecules thereof
EP06704788A EP1844069A4 (fr) 2005-01-28 2006-01-27 Molécules et leurs molécules chimériques
CA002596537A CA2596537A1 (fr) 2005-01-28 2006-01-27 Molecules et leurs molecules chimeriques

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US60/647,758 2005-01-28
US60/648,158 2005-01-28
US65328405P 2005-02-14 2005-02-14
US60/653,284 2005-02-14
US66246505P 2005-03-15 2005-03-15
US60/662,465 2005-03-15
US66555605P 2005-03-24 2005-03-24
US60/665,556 2005-03-24
US67071505P 2005-04-12 2005-04-12
US60/670,715 2005-04-12
US67604605P 2005-04-29 2005-04-29
US60/676,046 2005-04-29
US67708805P 2005-05-02 2005-05-02
US60/677,088 2005-05-02
AU2005906366 2005-11-16
AU2005906366A AU2005906366A0 (en) 2005-11-16 Tumor necrosis factor alpha and chimeric molecule thereof
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AU2005906750A AU2005906750A0 (en) 2005-12-01 Lymphotoxin alpha and chimeric molecule thereof

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US8722615B2 (en) 2009-12-02 2014-05-13 Acceleron Pharma, Inc. Compositions and methods for increasing serum half-life
US8883982B2 (en) 2011-06-08 2014-11-11 Acceleron Pharma, Inc. Compositions and methods for increasing serum half-life
US20160222082A1 (en) * 2013-09-18 2016-08-04 Levicept Ltd Fusion protein
US9567605B2 (en) 2010-01-05 2017-02-14 Vascular Biogenics Ltd. Methods for use of a specific anti-angiogenic adenoviral agent
WO2017068180A1 (fr) * 2015-10-23 2017-04-27 Apogenix Ag Protéines agonistes du récepteur light à chaîne unique
US9764000B2 (en) 2012-03-14 2017-09-19 Levicept Ltd Therapeutic use of p75NTR neurotrophin binding protein
US10369196B2 (en) 2010-01-05 2019-08-06 Vascular Biogenics Ltd. Compositions and methods for treating glioblastoma GBM
US10683339B2 (en) 2015-03-19 2020-06-16 Levicept Limited P75NTR binding protein-Fc fusion protein and methods of treating pain
US20210046156A1 (en) * 2018-01-18 2021-02-18 Fred Hutchinson Cancer Research Cente Altering inflammatory states of immune cells in vivo by modulating cellular activation states
US11339202B2 (en) 2014-07-17 2022-05-24 Levicept Limited Therapeutic use of p75NTR neurotrophin binding protein

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US8722615B2 (en) 2009-12-02 2014-05-13 Acceleron Pharma, Inc. Compositions and methods for increasing serum half-life
US10369196B2 (en) 2010-01-05 2019-08-06 Vascular Biogenics Ltd. Compositions and methods for treating glioblastoma GBM
US9567605B2 (en) 2010-01-05 2017-02-14 Vascular Biogenics Ltd. Methods for use of a specific anti-angiogenic adenoviral agent
US20130052165A1 (en) * 2010-01-12 2013-02-28 Livnat Bangio Methods of Producing Adenovirus Vectors and Viral Preparations Generated Thereby
US8883982B2 (en) 2011-06-08 2014-11-11 Acceleron Pharma, Inc. Compositions and methods for increasing serum half-life
US10751389B2 (en) 2012-03-14 2020-08-25 Levicept LLD Therapeutic use of p75NTR neurotrophin binding protein
US9764000B2 (en) 2012-03-14 2017-09-19 Levicept Ltd Therapeutic use of p75NTR neurotrophin binding protein
US9873728B2 (en) * 2013-09-18 2018-01-23 Levicept Ltd. p75NTR(NBP) fusion proteins and use of treating symptoms of pain
US20180273603A1 (en) * 2013-09-18 2018-09-27 Levicept Limited Fusion protein
US20160222082A1 (en) * 2013-09-18 2016-08-04 Levicept Ltd Fusion protein
US10988526B2 (en) 2013-09-18 2021-04-27 Levicept Limited DNA molecule encoding a p75NTR(NBP)-Fc fusion protein
US11339202B2 (en) 2014-07-17 2022-05-24 Levicept Limited Therapeutic use of p75NTR neurotrophin binding protein
US10683339B2 (en) 2015-03-19 2020-06-16 Levicept Limited P75NTR binding protein-Fc fusion protein and methods of treating pain
WO2017068180A1 (fr) * 2015-10-23 2017-04-27 Apogenix Ag Protéines agonistes du récepteur light à chaîne unique
US10683332B2 (en) 2015-10-23 2020-06-16 Apogenix Ag Single-chain light receptor agonist proteins
US20210046156A1 (en) * 2018-01-18 2021-02-18 Fred Hutchinson Cancer Research Cente Altering inflammatory states of immune cells in vivo by modulating cellular activation states

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